From 293e9af5f8b477d1875c8cba8ea7a616a2fbbe6b Mon Sep 17 00:00:00 2001 From: ShixiangWang Date: Wed, 13 Mar 2024 10:54:24 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Shixiang?= =?UTF-8?q?Wang/sigminer@ec7805cbc8643c9bb9522c2273ac4bdca2c3518b=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/cnsignature.html | 127 +- articles/sigminer.html | 5 +- news/index.html | 5 +- pkgdown.yml | 2 +- reference/bp.html | 602 +++---- reference/get_group_comparison.html | 16 +- reference/get_groups.html | 46 +- reference/get_pLOH_score.html | 58 +- reference/read_copynumber.html | 170 +- reference/read_maf.html | 2 +- reference/read_vcf.html | 2 +- reference/read_xena_variants.html | 47 +- reference/show_group_comparison.html | 16 +- reference/show_group_enrichment.html | 5 +- reference/show_sig_bootstrap.html | 2272 ++++++++++++------------ reference/sig_auto_extract.html | 52 +- reference/sig_estimate.html | 16 +- reference/sig_fit.html | 164 +- reference/sig_fit_bootstrap.html | 32 +- reference/sig_fit_bootstrap_batch.html | 104 +- reference/sig_tally.html | 132 +- reference/sigminer-package.html | 2 + 22 files changed, 1944 insertions(+), 1933 deletions(-) diff --git a/articles/cnsignature.html b/articles/cnsignature.html index 01c2bf1c..6efe6553 100644 --- a/articles/cnsignature.html +++ b/articles/cnsignature.html @@ -93,7 +93,7 @@

Analyze Copy Number Signatures with

Shixiang Wang ( )

-

2024-03-08

+

2024-03-13

Source: vignettes/cnsignature.Rmd @@ -111,6 +111,9 @@

2024-03-08

 library(sigminer)
+#> Registered S3 method overwritten by 'sigminer':
+#>   method      from
+#>   print.bytes Rcpp
 #> sigminer version 2.3.1
 #> - Star me at https://github.com/ShixiangWang/sigminer
 #> - Run hello() to see usage and citation.
@@ -137,36 +140,36 @@

Generate allele-specific c seg_cols = c("chromosome", "start", "end", "segVal"), genome_measure = "wg", complement = TRUE, add_loh = TRUE ) -#> ℹ [2024-03-08 02:38:33.929148]: Started. -#> ℹ [2024-03-08 02:38:33.940258]: Genome build : hg19. -#> ℹ [2024-03-08 02:38:33.941687]: Genome measure: wg. -#> ℹ [2024-03-08 02:38:33.943733]: When add_loh is TRUE, use_all is forced to TRUE. +#> ℹ [2024-03-13 10:54:09.194394]: Started. +#> ℹ [2024-03-13 10:54:09.205874]: Genome build : hg19. +#> ℹ [2024-03-13 10:54:09.215004]: Genome measure: wg. +#> ℹ [2024-03-13 10:54:09.216833]: When add_loh is TRUE, use_all is forced to TRUE. #> Please drop columns you don't want to keep before reading. -#> ✔ [2024-03-08 02:38:33.970988]: Chromosome size database for build obtained. -#> ℹ [2024-03-08 02:38:33.972522]: Reading input. -#> ✔ [2024-03-08 02:38:33.973955]: A data frame as input detected. -#> ✔ [2024-03-08 02:38:33.975731]: Column names checked. -#> ✔ [2024-03-08 02:38:33.977599]: Column order set. -#> ✔ [2024-03-08 02:38:33.986076]: Chromosomes unified. -#> ✔ [2024-03-08 02:38:34.00152]: Value 2 (normal copy) filled to uncalled chromosomes. -#> ✔ [2024-03-08 02:38:34.005961]: Data imported. -#> ℹ [2024-03-08 02:38:34.007438]: Segments info: -#> ℹ [2024-03-08 02:38:34.008844]: Keep - 477 -#> ℹ [2024-03-08 02:38:34.010228]: Drop - 0 -#> ✔ [2024-03-08 02:38:34.0121]: Segments sorted. -#> ℹ [2024-03-08 02:38:34.013502]: Adding LOH labels... -#> ℹ [2024-03-08 02:38:34.015682]: Joining adjacent segments with same copy number value. Be patient... -#> ✔ [2024-03-08 02:38:34.128215]: 410 segments left after joining. -#> ✔ [2024-03-08 02:38:34.130182]: Segmental table cleaned. -#> ℹ [2024-03-08 02:38:34.131609]: Annotating. -#> ✔ [2024-03-08 02:38:34.145737]: Annotation done. -#> ℹ [2024-03-08 02:38:34.147218]: Summarizing per sample. -#> ✔ [2024-03-08 02:38:34.166869]: Summarized. -#> ℹ [2024-03-08 02:38:34.168292]: Generating CopyNumber object. -#> ✔ [2024-03-08 02:38:34.170178]: Generated. -#> ℹ [2024-03-08 02:38:34.171587]: Validating object. -#> ✔ [2024-03-08 02:38:34.173034]: Done. -#> ℹ [2024-03-08 02:38:34.174754]: 0.246 secs elapsed. +#> ✔ [2024-03-13 10:54:09.229848]: Chromosome size database for build obtained. +#> ℹ [2024-03-13 10:54:09.231774]: Reading input. +#> ✔ [2024-03-13 10:54:09.233324]: A data frame as input detected. +#> ✔ [2024-03-13 10:54:09.235187]: Column names checked. +#> ✔ [2024-03-13 10:54:09.237252]: Column order set. +#> ✔ [2024-03-13 10:54:09.245748]: Chromosomes unified. +#> ✔ [2024-03-13 10:54:09.2618]: Value 2 (normal copy) filled to uncalled chromosomes. +#> ✔ [2024-03-13 10:54:09.266716]: Data imported. +#> ℹ [2024-03-13 10:54:09.268426]: Segments info: +#> ℹ [2024-03-13 10:54:09.269901]: Keep - 477 +#> ℹ [2024-03-13 10:54:09.271384]: Drop - 0 +#> ✔ [2024-03-13 10:54:09.273401]: Segments sorted. +#> ℹ [2024-03-13 10:54:09.274818]: Adding LOH labels... +#> ℹ [2024-03-13 10:54:09.27717]: Joining adjacent segments with same copy number value. Be patient... +#> ✔ [2024-03-13 10:54:09.39557]: 410 segments left after joining. +#> ✔ [2024-03-13 10:54:09.39772]: Segmental table cleaned. +#> ℹ [2024-03-13 10:54:09.399427]: Annotating. +#> ✔ [2024-03-13 10:54:09.414763]: Annotation done. +#> ℹ [2024-03-13 10:54:09.416555]: Summarizing per sample. +#> ✔ [2024-03-13 10:54:09.43881]: Summarized. +#> ℹ [2024-03-13 10:54:09.440522]: Generating CopyNumber object. +#> ✔ [2024-03-13 10:54:09.442545]: Generated. +#> ℹ [2024-03-13 10:54:09.444029]: Validating object. +#> ✔ [2024-03-13 10:54:09.445553]: Done. +#> ℹ [2024-03-13 10:54:09.447419]: 0.253 secs elapsed. 
 cn
 #> An object of class CopyNumber 
@@ -232,10 +235,10 @@ 
Classify the segments wi
 
 
 tally_s <- sig_tally(cn, method = "S")
-#> ℹ [2024-03-08 02:38:34.315256]: Started.
-#> ℹ [2024-03-08 02:38:34.319123]: When you use method 'S', please make sure you have set 'join_adj_seg' to FALSE and 'add_loh' to TRUE in 'read_copynumber() in the previous step!
-#> ✔ [2024-03-08 02:38:34.333496]: Matrix generated.
-#> ℹ [2024-03-08 02:38:34.335059]: 0.02 secs elapsed.
+#> ℹ [2024-03-13 10:54:09.595514]: Started.
+#> ℹ [2024-03-13 10:54:09.599915]: When you use method 'S', please make sure you have set 'join_adj_seg' to FALSE and 'add_loh' to TRUE in 'read_copynumber() in the previous step!
+#> ✔ [2024-03-13 10:54:09.614944]: Matrix generated.
+#> ℹ [2024-03-13 10:54:09.616762]: 0.021 secs elapsed.
 
 str(tally_s$all_matrices, max.level = 1)
 #> List of 2
@@ -266,35 +269,35 @@ 
Refit (19) reference signatures
 act_refit = sig_fit(t(tally_s$all_matrices$CN_48), sig_index = "ALL", sig_db = "CNS_TCGA")
-#> ℹ [2024-03-08 02:38:35.06833]: Started.
-#> ✔ [2024-03-08 02:38:35.069978]: Signature index detected.
-#> ℹ [2024-03-08 02:38:35.071365]: Checking signature database in package.
-#> ℹ [2024-03-08 02:38:35.073651]: Checking signature index.
-#> ℹ [2024-03-08 02:38:35.075085]: Valid index for db 'CNS_TCGA':
+#> ℹ [2024-03-13 10:54:10.442349]: Started.
+#> ✔ [2024-03-13 10:54:10.444184]: Signature index detected.
+#> ℹ [2024-03-13 10:54:10.445601]: Checking signature database in package.
+#> ℹ [2024-03-13 10:54:10.448011]: Checking signature index.
+#> ℹ [2024-03-13 10:54:10.449447]: Valid index for db 'CNS_TCGA':
 #> CN1 CN2 CN3 CN4 CN5 CN6 CN7 CN8 CN9 CN10 CN11 CN12 CN13 CN14 CN15 CN16 CN17 CN18 CN19
-#> ✔ [2024-03-08 02:38:35.07655]: Database and index checked.
-#> ✔ [2024-03-08 02:38:35.078058]: Signature normalized.
-#> ℹ [2024-03-08 02:38:35.079419]: Checking row number for catalog matrix and signature matrix.
-#> ✔ [2024-03-08 02:38:35.080745]: Checked.
-#> ℹ [2024-03-08 02:38:35.082067]: Checking rownames for catalog matrix and signature matrix.
-#> ✔ [2024-03-08 02:38:35.08345]: Checked.
-#> ✔ [2024-03-08 02:38:35.084776]: Method 'QP' detected.
-#> ✔ [2024-03-08 02:38:35.088407]: Corresponding function generated.
-#> ℹ [2024-03-08 02:38:35.089792]: Calling function.
-#> ℹ [2024-03-08 02:38:35.091556]: Fitting sample: TCGA-05-4417-01A-22D-1854-01
-#> ℹ [2024-03-08 02:38:35.093209]: Fitting sample: TCGA-06-0644-01A-02D-0310-01
-#> ℹ [2024-03-08 02:38:35.09467]: Fitting sample: TCGA-19-2621-01B-01D-0911-01
-#> ℹ [2024-03-08 02:38:35.096157]: Fitting sample: TCGA-26-6174-01A-21D-1842-01
-#> ℹ [2024-03-08 02:38:35.097594]: Fitting sample: TCGA-99-7458-01A-11D-2035-01
-#> ℹ [2024-03-08 02:38:35.09905]: Fitting sample: TCGA-A5-A0G2-01A-11D-A042-01
-#> ℹ [2024-03-08 02:38:35.100483]: Fitting sample: TCGA-A8-A07S-01A-11D-A036-01
-#> ℹ [2024-03-08 02:38:35.10191]: Fitting sample: TCGA-B6-A0X5-01A-21D-A107-01
-#> ℹ [2024-03-08 02:38:35.103387]: Fitting sample: TCGA-CV-7432-01A-11D-2128-01
-#> ℹ [2024-03-08 02:38:35.104853]: Fitting sample: TCGA-DF-A2KN-01A-11D-A17U-01
-#> ✔ [2024-03-08 02:38:35.1063]: Done.
-#> ℹ [2024-03-08 02:38:35.107668]: Generating output signature exposures.
-#> ✔ [2024-03-08 02:38:35.109622]: Done.
-#> ℹ [2024-03-08 02:38:35.111053]: 0.043 secs elapsed.

+#> ✔ [2024-03-13 10:54:10.45095]: Database and index checked.
+#> ✔ [2024-03-13 10:54:10.452586]: Signature normalized.
+#> ℹ [2024-03-13 10:54:10.45398]: Checking row number for catalog matrix and signature matrix.
+#> ✔ [2024-03-13 10:54:10.455415]: Checked.
+#> ℹ [2024-03-13 10:54:10.456789]: Checking rownames for catalog matrix and signature matrix.
+#> ✔ [2024-03-13 10:54:10.458151]: Checked.
+#> ✔ [2024-03-13 10:54:10.45951]: Method 'QP' detected.
+#> ✔ [2024-03-13 10:54:10.463385]: Corresponding function generated.
+#> ℹ [2024-03-13 10:54:10.464819]: Calling function.
+#> ℹ [2024-03-13 10:54:10.466643]: Fitting sample: TCGA-05-4417-01A-22D-1854-01
+#> ℹ [2024-03-13 10:54:10.468404]: Fitting sample: TCGA-06-0644-01A-02D-0310-01
+#> ℹ [2024-03-13 10:54:10.469913]: Fitting sample: TCGA-19-2621-01B-01D-0911-01
+#> ℹ [2024-03-13 10:54:10.471416]: Fitting sample: TCGA-26-6174-01A-21D-1842-01
+#> ℹ [2024-03-13 10:54:10.472881]: Fitting sample: TCGA-99-7458-01A-11D-2035-01
+#> ℹ [2024-03-13 10:54:10.474342]: Fitting sample: TCGA-A5-A0G2-01A-11D-A042-01
+#> ℹ [2024-03-13 10:54:10.475837]: Fitting sample: TCGA-A8-A07S-01A-11D-A036-01
+#> ℹ [2024-03-13 10:54:10.477284]: Fitting sample: TCGA-B6-A0X5-01A-21D-A107-01
+#> ℹ [2024-03-13 10:54:10.478809]: Fitting sample: TCGA-CV-7432-01A-11D-2128-01
+#> ℹ [2024-03-13 10:54:10.480316]: Fitting sample: TCGA-DF-A2KN-01A-11D-A17U-01
+#> ✔ [2024-03-13 10:54:10.481794]: Done.
+#> ℹ [2024-03-13 10:54:10.483193]: Generating output signature exposures.
+#> ✔ [2024-03-13 10:54:10.485302]: Done.
+#> ℹ [2024-03-13 10:54:10.486758]: 0.044 secs elapsed.

We can use some threshold to keep really contributed signautres.

 act_refit2 = act_refit[apply(act_refit, 1, function(x) sum(x) > 0.1),]
diff --git a/articles/sigminer.html b/articles/sigminer.html
index 8ef0e85a..ed0bf025 100644
--- a/articles/sigminer.html
+++ b/articles/sigminer.html
@@ -92,7 +92,7 @@ 
A Quick Start of sigminer Package

                         
Shixiang Wang (
  )

             
-            
2024-03-08

+            
2024-03-13

       
       Source: vignettes/sigminer.Rmd
       
@@ -105,6 +105,9 @@ 
2024-03-08

 like below:

 
 library(sigminer)
+#> Registered S3 method overwritten by 'sigminer':
+#>   method      from
+#>   print.bytes Rcpp
 #> sigminer version 2.3.1
 #> - Star me at https://github.com/ShixiangWang/sigminer
 #> - Run hello() to see usage and citation.
diff --git a/news/index.html b/news/index.html
index ba766cad..8ef6002f 100644
--- a/news/index.html
+++ b/news/index.html
@@ -62,8 +62,9 @@ 
Changelog 

 
     

 
sigminer 2.3.1

-
    • Fixed the error in generating DBS and INDEL matrix when only one sample input (#453).
      • 
-
    • 
+
    • Added cluster_col to show_group_enrichment().
      • 
+
    • Fixed the bug that error returned when cluster_row = TRUE & return_list = TRUE in function show_group_enrichment().
      • 
+
    • Fixed the error in generating DBS and INDEL matrix when only one sample input (#453).
      • 
 

     

 
sigminer 2.3.02023-12-12

diff --git a/pkgdown.yml b/pkgdown.yml
index 7f8c4336..4ff30881 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   cnsignature: cnsignature.html
   sigminer: sigminer.html
-last_built: 2024-03-08T02:30Z
+last_built: 2024-03-13T10:44Z
 urls:
   reference: https://shixiangwang.github.io/sigminer/reference
   article: https://shixiangwang.github.io/sigminer/articles
diff --git a/reference/bp.html b/reference/bp.html
index 0855fb25..887e30b6 100644
--- a/reference/bp.html
+++ b/reference/bp.html
@@ -1230,12 +1230,12 @@ 
Examples

 # try to optimize the result.
 # NOTE: the optimization step may not truly optimize the result!
 expo <- bp_attribute_activity(e1, return_class = "data.table")
-#> Set cache dir: /tmp/RtmpXZeTRm/sigminer_attribute_activity
+#> Set cache dir: /tmp/RtmpT86DiN/sigminer_attribute_activity
 #> Handling sample: Sample_2
-#> ℹ [2024-03-08 02:30:12.832891]: Started.
-#> ℹ [2024-03-08 02:30:12.844429]: Checking catalog.
-#> ✔ [2024-03-08 02:30:12.845957]: Done.
-#> ℹ [2024-03-08 02:30:12.847361]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:33.384344]: Started.
+#> ℹ [2024-03-13 10:44:33.402215]: Checking catalog.
+#> ✔ [2024-03-13 10:44:33.403677]: Done.
+#> ℹ [2024-03-13 10:44:33.404999]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -1339,17 +1339,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:16.410059]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:16.411708]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:16.413101]: Done.
-#> ℹ [2024-03-08 02:30:16.414514]: 3.582 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_2_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_2_sim.rds
+#> ✔ [2024-03-13 10:44:36.878234]: Signature exposures collected.
+#> ✔ [2024-03-13 10:44:36.87988]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:44:36.881269]: Done.
+#> ℹ [2024-03-13 10:44:36.882688]: 3.499 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_2_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_2_sim.rds
 #> Handling sample: Sample_3
-#> ℹ [2024-03-08 02:30:16.58538]: Started.
-#> ℹ [2024-03-08 02:30:16.587828]: Checking catalog.
-#> ✔ [2024-03-08 02:30:16.589418]: Done.
-#> ℹ [2024-03-08 02:30:16.590953]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:37.059309]: Started.
+#> ℹ [2024-03-13 10:44:37.061371]: Checking catalog.
+#> ✔ [2024-03-13 10:44:37.062906]: Done.
+#> ℹ [2024-03-13 10:44:37.064434]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -1453,17 +1453,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:19.985197]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:19.986916]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:19.988317]: Done.
-#> ℹ [2024-03-08 02:30:19.989734]: 3.404 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_3_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_3_sim.rds
+#> ✔ [2024-03-13 10:44:40.409362]: Signature exposures collected.
+#> ✔ [2024-03-13 10:44:40.410936]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:44:40.41234]: Done.
+#> ℹ [2024-03-13 10:44:40.413756]: 3.354 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_3_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_3_sim.rds
 #> Handling sample: Sample_4
-#> ℹ [2024-03-08 02:30:20.164483]: Started.
-#> ℹ [2024-03-08 02:30:20.166303]: Checking catalog.
-#> ✔ [2024-03-08 02:30:20.167689]: Done.
-#> ℹ [2024-03-08 02:30:20.169024]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:40.591209]: Started.
+#> ℹ [2024-03-13 10:44:40.593165]: Checking catalog.
+#> ✔ [2024-03-13 10:44:40.594838]: Done.
+#> ℹ [2024-03-13 10:44:40.596457]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -1567,17 +1567,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:23.535574]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:23.537142]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:23.538522]: Done.
-#> ℹ [2024-03-08 02:30:23.539946]: 3.375 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_4_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_4_sim.rds
+#> ✔ [2024-03-13 10:44:43.948533]: Signature exposures collected.
+#> ✔ [2024-03-13 10:44:43.950074]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:44:43.951474]: Done.
+#> ℹ [2024-03-13 10:44:43.952887]: 3.362 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_4_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_4_sim.rds
 #> Handling sample: Sample_5
-#> ℹ [2024-03-08 02:30:23.705806]: Started.
-#> ℹ [2024-03-08 02:30:23.707777]: Checking catalog.
-#> ✔ [2024-03-08 02:30:23.709477]: Done.
-#> ℹ [2024-03-08 02:30:23.711141]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:44.115873]: Started.
+#> ℹ [2024-03-13 10:44:44.117708]: Checking catalog.
+#> ✔ [2024-03-13 10:44:44.119335]: Done.
+#> ℹ [2024-03-13 10:44:44.120808]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -1681,17 +1681,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:26.992111]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:26.993671]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:26.995077]: Done.
-#> ℹ [2024-03-08 02:30:26.996507]: 3.291 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_5_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_5_sim.rds
+#> ✔ [2024-03-13 10:44:47.409122]: Signature exposures collected.
+#> ✔ [2024-03-13 10:44:47.410697]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:44:47.412175]: Done.
+#> ℹ [2024-03-13 10:44:47.413649]: 3.298 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_5_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_5_sim.rds
 #> Handling sample: Sample_6
-#> ℹ [2024-03-08 02:30:27.160037]: Started.
-#> ℹ [2024-03-08 02:30:27.161948]: Checking catalog.
-#> ✔ [2024-03-08 02:30:27.163667]: Done.
-#> ℹ [2024-03-08 02:30:27.165277]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:47.582448]: Started.
+#> ℹ [2024-03-13 10:44:47.584351]: Checking catalog.
+#> ✔ [2024-03-13 10:44:47.585963]: Done.
+#> ℹ [2024-03-13 10:44:47.587553]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -1795,17 +1795,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:30.434272]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:30.43585]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:30.437226]: Done.
-#> ℹ [2024-03-08 02:30:30.438629]: 3.279 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_6_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_6_sim.rds
+#> ✔ [2024-03-13 10:44:50.902768]: Signature exposures collected.
+#> ✔ [2024-03-13 10:44:50.904457]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:44:50.905871]: Done.
+#> ℹ [2024-03-13 10:44:50.907347]: 3.325 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_6_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_6_sim.rds
 #> Handling sample: Sample_7
-#> ℹ [2024-03-08 02:30:30.605855]: Started.
-#> ℹ [2024-03-08 02:30:30.607842]: Checking catalog.
-#> ✔ [2024-03-08 02:30:30.609551]: Done.
-#> ℹ [2024-03-08 02:30:30.611199]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:51.076984]: Started.
+#> ℹ [2024-03-13 10:44:51.078849]: Checking catalog.
+#> ✔ [2024-03-13 10:44:51.080467]: Done.
+#> ℹ [2024-03-13 10:44:51.082]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -1909,17 +1909,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:34.057022]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:34.058561]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:34.05993]: Done.
-#> ℹ [2024-03-08 02:30:34.061307]: 3.455 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_7_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_7_sim.rds
+#> ✔ [2024-03-13 10:44:54.408537]: Signature exposures collected.
+#> ✔ [2024-03-13 10:44:54.410134]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:44:54.411551]: Done.
+#> ℹ [2024-03-13 10:44:54.412981]: 3.336 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_7_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_7_sim.rds
 #> Handling sample: Sample_8
-#> ℹ [2024-03-08 02:30:34.223204]: Started.
-#> ℹ [2024-03-08 02:30:34.225001]: Checking catalog.
-#> ✔ [2024-03-08 02:30:34.226358]: Done.
-#> ℹ [2024-03-08 02:30:34.227736]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:54.594308]: Started.
+#> ℹ [2024-03-13 10:44:54.596181]: Checking catalog.
+#> ✔ [2024-03-13 10:44:54.597749]: Done.
+#> ℹ [2024-03-13 10:44:54.599249]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2023,17 +2023,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:37.508814]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:37.510373]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:37.511769]: Done.
-#> ℹ [2024-03-08 02:30:37.51316]: 3.29 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_8_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_8_sim.rds
+#> ✔ [2024-03-13 10:44:58.046692]: Signature exposures collected.
+#> ✔ [2024-03-13 10:44:58.049279]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:44:58.051466]: Done.
+#> ℹ [2024-03-13 10:44:58.053525]: 3.459 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_8_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_8_sim.rds
 #> Handling sample: Sample_9
-#> ℹ [2024-03-08 02:30:37.673634]: Started.
-#> ℹ [2024-03-08 02:30:37.675586]: Checking catalog.
-#> ✔ [2024-03-08 02:30:37.677229]: Done.
-#> ℹ [2024-03-08 02:30:37.678781]: About to start bootstrap.
+#> ℹ [2024-03-13 10:44:58.221839]: Started.
+#> ℹ [2024-03-13 10:44:58.223753]: Checking catalog.
+#> ✔ [2024-03-13 10:44:58.225356]: Done.
+#> ℹ [2024-03-13 10:44:58.226848]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2137,17 +2137,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:41.013271]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:41.014864]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:41.016347]: Done.
-#> ℹ [2024-03-08 02:30:41.01777]: 3.344 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_9_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_9_sim.rds
+#> ✔ [2024-03-13 10:45:01.609521]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:01.611078]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:01.612525]: Done.
+#> ℹ [2024-03-13 10:45:01.613933]: 3.392 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_9_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_9_sim.rds
 #> Handling sample: Sample_10
-#> ℹ [2024-03-08 02:30:41.181307]: Started.
-#> ℹ [2024-03-08 02:30:41.183225]: Checking catalog.
-#> ✔ [2024-03-08 02:30:41.184814]: Done.
-#> ℹ [2024-03-08 02:30:41.18633]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:01.792337]: Started.
+#> ℹ [2024-03-13 10:45:01.794571]: Checking catalog.
+#> ✔ [2024-03-13 10:45:01.796214]: Done.
+#> ℹ [2024-03-13 10:45:01.79772]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2251,17 +2251,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:44.537519]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:44.539122]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:44.540503]: Done.
-#> ℹ [2024-03-08 02:30:44.541916]: 3.361 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_10_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_10_sim.rds
+#> ✔ [2024-03-13 10:45:05.196443]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:05.198018]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:05.199423]: Done.
+#> ℹ [2024-03-13 10:45:05.200831]: 3.408 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_10_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_10_sim.rds
 #> Handling sample: Sample_11
-#> ℹ [2024-03-08 02:30:44.703062]: Started.
-#> ℹ [2024-03-08 02:30:44.704991]: Checking catalog.
-#> ✔ [2024-03-08 02:30:44.706596]: Done.
-#> ℹ [2024-03-08 02:30:44.708161]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:05.368154]: Started.
+#> ℹ [2024-03-13 10:45:05.370059]: Checking catalog.
+#> ✔ [2024-03-13 10:45:05.371738]: Done.
+#> ℹ [2024-03-13 10:45:05.373285]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2365,17 +2365,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:48.022743]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:48.024352]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:48.025743]: Done.
-#> ℹ [2024-03-08 02:30:48.027189]: 3.324 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_11_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_11_sim.rds
+#> ✔ [2024-03-13 10:45:08.709585]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:08.711186]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:08.712615]: Done.
+#> ℹ [2024-03-13 10:45:08.714073]: 3.346 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_11_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_11_sim.rds
 #> Handling sample: Sample_13
-#> ℹ [2024-03-08 02:30:48.1922]: Started.
-#> ℹ [2024-03-08 02:30:48.194145]: Checking catalog.
-#> ✔ [2024-03-08 02:30:48.195818]: Done.
-#> ℹ [2024-03-08 02:30:48.19738]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:08.886259]: Started.
+#> ℹ [2024-03-13 10:45:08.888441]: Checking catalog.
+#> ✔ [2024-03-13 10:45:08.890254]: Done.
+#> ℹ [2024-03-13 10:45:08.892028]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2479,17 +2479,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:51.485024]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:51.486622]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:51.488053]: Done.
-#> ℹ [2024-03-08 02:30:51.48948]: 3.297 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_13_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_13_sim.rds
+#> ✔ [2024-03-13 10:45:12.24016]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:12.24171]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:12.243073]: Done.
+#> ℹ [2024-03-13 10:45:12.244501]: 3.358 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_13_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_13_sim.rds
 #> Handling sample: Sample_14
-#> ℹ [2024-03-08 02:30:51.654396]: Started.
-#> ℹ [2024-03-08 02:30:51.656223]: Checking catalog.
-#> ✔ [2024-03-08 02:30:51.657648]: Done.
-#> ℹ [2024-03-08 02:30:51.659047]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:12.424399]: Started.
+#> ℹ [2024-03-13 10:45:12.426261]: Checking catalog.
+#> ✔ [2024-03-13 10:45:12.427869]: Done.
+#> ℹ [2024-03-13 10:45:12.429364]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2593,17 +2593,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:54.979623]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:54.981196]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:54.98259]: Done.
-#> ℹ [2024-03-08 02:30:54.984029]: 3.33 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_14_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_14_sim.rds
+#> ✔ [2024-03-13 10:45:15.764419]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:15.766167]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:15.76762]: Done.
+#> ℹ [2024-03-13 10:45:15.769106]: 3.345 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_14_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_14_sim.rds
 #> Handling sample: Sample_15
-#> ℹ [2024-03-08 02:30:55.149054]: Started.
-#> ℹ [2024-03-08 02:30:55.151087]: Checking catalog.
-#> ✔ [2024-03-08 02:30:55.152814]: Done.
-#> ℹ [2024-03-08 02:30:55.154405]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:15.936532]: Started.
+#> ℹ [2024-03-13 10:45:15.938415]: Checking catalog.
+#> ✔ [2024-03-13 10:45:15.940079]: Done.
+#> ℹ [2024-03-13 10:45:15.941617]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2707,17 +2707,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:30:58.66462]: Signature exposures collected.
-#> ✔ [2024-03-08 02:30:58.666535]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:30:58.667951]: Done.
-#> ℹ [2024-03-08 02:30:58.669358]: 3.52 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_15_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_15_sim.rds
+#> ✔ [2024-03-13 10:45:19.340762]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:19.342341]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:19.343751]: Done.
+#> ℹ [2024-03-13 10:45:19.345168]: 3.409 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_15_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_15_sim.rds
 #> Handling sample: Sample_16
-#> ℹ [2024-03-08 02:30:58.83148]: Started.
-#> ℹ [2024-03-08 02:30:58.833452]: Checking catalog.
-#> ✔ [2024-03-08 02:30:58.835078]: Done.
-#> ℹ [2024-03-08 02:30:58.836586]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:19.521857]: Started.
+#> ℹ [2024-03-13 10:45:19.523846]: Checking catalog.
+#> ✔ [2024-03-13 10:45:19.525525]: Done.
+#> ℹ [2024-03-13 10:45:19.527115]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2821,17 +2821,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:02.200853]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:02.202455]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:02.203895]: Done.
-#> ℹ [2024-03-08 02:31:02.205326]: 3.374 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_16_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_16_sim.rds
+#> ✔ [2024-03-13 10:45:22.927139]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:22.928778]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:22.930167]: Done.
+#> ℹ [2024-03-13 10:45:22.931627]: 3.41 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_16_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_16_sim.rds
 #> Handling sample: Sample_18
-#> ℹ [2024-03-08 02:31:02.370713]: Started.
-#> ℹ [2024-03-08 02:31:02.372726]: Checking catalog.
-#> ✔ [2024-03-08 02:31:02.374384]: Done.
-#> ℹ [2024-03-08 02:31:02.375974]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:23.11008]: Started.
+#> ℹ [2024-03-13 10:45:23.112176]: Checking catalog.
+#> ✔ [2024-03-13 10:45:23.113968]: Done.
+#> ℹ [2024-03-13 10:45:23.115703]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -2935,17 +2935,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:05.704674]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:05.706299]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:05.707751]: Done.
-#> ℹ [2024-03-08 02:31:05.709199]: 3.338 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_18_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_18_sim.rds
+#> ✔ [2024-03-13 10:45:26.633155]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:26.634817]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:26.636259]: Done.
+#> ℹ [2024-03-13 10:45:26.637706]: 3.528 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_18_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_18_sim.rds
 #> Handling sample: Sample_20
-#> ℹ [2024-03-08 02:31:05.873744]: Started.
-#> ℹ [2024-03-08 02:31:05.875749]: Checking catalog.
-#> ✔ [2024-03-08 02:31:05.877421]: Done.
-#> ℹ [2024-03-08 02:31:05.879013]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:26.80957]: Started.
+#> ℹ [2024-03-13 10:45:26.811525]: Checking catalog.
+#> ✔ [2024-03-13 10:45:26.813137]: Done.
+#> ℹ [2024-03-13 10:45:26.814692]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3049,17 +3049,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:09.158381]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:09.159994]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:09.161406]: Done.
-#> ℹ [2024-03-08 02:31:09.162886]: 3.289 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_20_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_20_sim.rds
+#> ✔ [2024-03-13 10:45:30.183278]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:30.184927]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:30.186352]: Done.
+#> ℹ [2024-03-13 10:45:30.187853]: 3.378 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_20_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_20_sim.rds
 #> Handling sample: Sample_21
-#> ℹ [2024-03-08 02:31:09.325221]: Started.
-#> ℹ [2024-03-08 02:31:09.327193]: Checking catalog.
-#> ✔ [2024-03-08 02:31:09.328848]: Done.
-#> ℹ [2024-03-08 02:31:09.330411]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:30.367824]: Started.
+#> ℹ [2024-03-13 10:45:30.369813]: Checking catalog.
+#> ✔ [2024-03-13 10:45:30.371536]: Done.
+#> ℹ [2024-03-13 10:45:30.373101]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3163,17 +3163,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:12.705755]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:12.707371]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:12.70878]: Done.
-#> ℹ [2024-03-08 02:31:12.710214]: 3.385 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_21_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_21_sim.rds
+#> ✔ [2024-03-13 10:45:33.845937]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:33.847552]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:33.848996]: Done.
+#> ℹ [2024-03-13 10:45:33.850447]: 3.483 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_21_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_21_sim.rds
 #> Handling sample: Sample_23
-#> ℹ [2024-03-08 02:31:12.876951]: Started.
-#> ℹ [2024-03-08 02:31:12.878953]: Checking catalog.
-#> ✔ [2024-03-08 02:31:12.880647]: Done.
-#> ℹ [2024-03-08 02:31:12.882227]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:34.024046]: Started.
+#> ℹ [2024-03-13 10:45:34.025988]: Checking catalog.
+#> ✔ [2024-03-13 10:45:34.027705]: Done.
+#> ℹ [2024-03-13 10:45:34.029305]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3277,17 +3277,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:16.18263]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:16.184272]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:16.185699]: Done.
-#> ℹ [2024-03-08 02:31:16.187163]: 3.31 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_23_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_23_sim.rds
+#> ✔ [2024-03-13 10:45:37.41644]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:37.41806]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:37.419502]: Done.
+#> ℹ [2024-03-13 10:45:37.420946]: 3.397 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_23_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_23_sim.rds
 #> Handling sample: Sample_25
-#> ℹ [2024-03-08 02:31:16.349211]: Started.
-#> ℹ [2024-03-08 02:31:16.351205]: Checking catalog.
-#> ✔ [2024-03-08 02:31:16.352871]: Done.
-#> ℹ [2024-03-08 02:31:16.354472]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:37.591743]: Started.
+#> ℹ [2024-03-13 10:45:37.593688]: Checking catalog.
+#> ✔ [2024-03-13 10:45:37.595356]: Done.
+#> ℹ [2024-03-13 10:45:37.596943]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3391,17 +3391,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:19.692632]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:19.694243]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:19.695702]: Done.
-#> ℹ [2024-03-08 02:31:19.697172]: 3.348 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_25_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_25_sim.rds
+#> ✔ [2024-03-13 10:45:41.028694]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:41.030319]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:41.031777]: Done.
+#> ℹ [2024-03-13 10:45:41.033272]: 3.442 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_25_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_25_sim.rds
 #> Handling sample: Sample_26
-#> ℹ [2024-03-08 02:31:19.859146]: Started.
-#> ℹ [2024-03-08 02:31:19.861051]: Checking catalog.
-#> ✔ [2024-03-08 02:31:19.862636]: Done.
-#> ℹ [2024-03-08 02:31:19.864158]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:41.221347]: Started.
+#> ℹ [2024-03-13 10:45:41.223342]: Checking catalog.
+#> ✔ [2024-03-13 10:45:41.224912]: Done.
+#> ℹ [2024-03-13 10:45:41.226548]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3505,17 +3505,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:23.245215]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:23.246747]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:23.248133]: Done.
-#> ℹ [2024-03-08 02:31:23.249522]: 3.39 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_26_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_26_sim.rds
+#> ✔ [2024-03-13 10:45:44.630965]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:44.632593]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:44.633993]: Done.
+#> ℹ [2024-03-13 10:45:44.635449]: 3.414 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_26_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_26_sim.rds
 #> Handling sample: Sample_27
-#> ℹ [2024-03-08 02:31:23.409005]: Started.
-#> ℹ [2024-03-08 02:31:23.410932]: Checking catalog.
-#> ✔ [2024-03-08 02:31:23.412562]: Done.
-#> ℹ [2024-03-08 02:31:23.414021]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:44.834393]: Started.
+#> ℹ [2024-03-13 10:45:44.836279]: Checking catalog.
+#> ✔ [2024-03-13 10:45:44.837921]: Done.
+#> ℹ [2024-03-13 10:45:44.839496]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3619,17 +3619,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:26.693348]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:26.694916]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:26.696301]: Done.
-#> ℹ [2024-03-08 02:31:26.697708]: 3.289 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_27_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_27_sim.rds
+#> ✔ [2024-03-13 10:45:48.260972]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:48.26261]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:48.264055]: Done.
+#> ℹ [2024-03-13 10:45:48.265538]: 3.431 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_27_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_27_sim.rds
 #> Handling sample: Sample_28
-#> ℹ [2024-03-08 02:31:26.857615]: Started.
-#> ℹ [2024-03-08 02:31:26.859611]: Checking catalog.
-#> ✔ [2024-03-08 02:31:26.861257]: Done.
-#> ℹ [2024-03-08 02:31:26.862835]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:48.470398]: Started.
+#> ℹ [2024-03-13 10:45:48.472556]: Checking catalog.
+#> ✔ [2024-03-13 10:45:48.474396]: Done.
+#> ℹ [2024-03-13 10:45:48.476202]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3733,17 +3733,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:30.077306]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:30.0789]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:30.080283]: Done.
-#> ℹ [2024-03-08 02:31:30.081696]: 3.224 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_28_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_28_sim.rds
+#> ✔ [2024-03-13 10:45:51.97397]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:51.975582]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:51.97699]: Done.
+#> ℹ [2024-03-13 10:45:51.978416]: 3.508 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_28_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_28_sim.rds
 #> Handling sample: Sample_29
-#> ℹ [2024-03-08 02:31:30.243956]: Started.
-#> ℹ [2024-03-08 02:31:30.245961]: Checking catalog.
-#> ✔ [2024-03-08 02:31:30.247679]: Done.
-#> ℹ [2024-03-08 02:31:30.249253]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:52.150234]: Started.
+#> ℹ [2024-03-13 10:45:52.152255]: Checking catalog.
+#> ✔ [2024-03-13 10:45:52.153845]: Done.
+#> ℹ [2024-03-13 10:45:52.155343]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3847,17 +3847,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:33.489635]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:33.491269]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:33.49267]: Done.
-#> ℹ [2024-03-08 02:31:33.49408]: 3.25 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_29_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_29_sim.rds
+#> ✔ [2024-03-13 10:45:55.49373]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:55.495461]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:55.496939]: Done.
+#> ℹ [2024-03-13 10:45:55.498469]: 3.348 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_29_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_29_sim.rds
 #> Handling sample: Sample_30
-#> ℹ [2024-03-08 02:31:33.652476]: Started.
-#> ℹ [2024-03-08 02:31:33.65449]: Checking catalog.
-#> ✔ [2024-03-08 02:31:33.656224]: Done.
-#> ℹ [2024-03-08 02:31:33.657963]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:55.687584]: Started.
+#> ℹ [2024-03-13 10:45:55.689469]: Checking catalog.
+#> ✔ [2024-03-13 10:45:55.691101]: Done.
+#> ℹ [2024-03-13 10:45:55.692654]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -3961,17 +3961,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:36.885162]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:36.886759]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:36.888171]: Done.
-#> ℹ [2024-03-08 02:31:36.889597]: 3.237 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_30_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_30_sim.rds
+#> ✔ [2024-03-13 10:45:58.978629]: Signature exposures collected.
+#> ✔ [2024-03-13 10:45:58.980304]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:45:58.981759]: Done.
+#> ℹ [2024-03-13 10:45:58.98324]: 3.296 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_30_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_30_sim.rds
 #> Handling sample: Sample_1
-#> ℹ [2024-03-08 02:31:37.047844]: Started.
-#> ℹ [2024-03-08 02:31:37.049782]: Checking catalog.
-#> ✔ [2024-03-08 02:31:37.051446]: Done.
-#> ℹ [2024-03-08 02:31:37.052961]: About to start bootstrap.
+#> ℹ [2024-03-13 10:45:59.147822]: Started.
+#> ℹ [2024-03-13 10:45:59.149813]: Checking catalog.
+#> ✔ [2024-03-13 10:45:59.151504]: Done.
+#> ℹ [2024-03-13 10:45:59.153048]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -4075,17 +4075,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:40.623919]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:40.625446]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:40.62684]: Done.
-#> ℹ [2024-03-08 02:31:40.628247]: 3.58 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_1_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_1_sim.rds
+#> ✔ [2024-03-13 10:46:02.877016]: Signature exposures collected.
+#> ✔ [2024-03-13 10:46:02.878726]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:46:02.880258]: Done.
+#> ℹ [2024-03-13 10:46:02.881743]: 3.734 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_1_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_1_sim.rds
 #> Handling sample: Sample_12
-#> ℹ [2024-03-08 02:31:40.78469]: Started.
-#> ℹ [2024-03-08 02:31:40.78666]: Checking catalog.
-#> ✔ [2024-03-08 02:31:40.788326]: Done.
-#> ℹ [2024-03-08 02:31:40.789913]: About to start bootstrap.
+#> ℹ [2024-03-13 10:46:03.056678]: Started.
+#> ℹ [2024-03-13 10:46:03.058627]: Checking catalog.
+#> ✔ [2024-03-13 10:46:03.060318]: Done.
+#> ℹ [2024-03-13 10:46:03.061917]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -4189,17 +4189,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:44.531768]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:44.533305]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:44.534665]: Done.
-#> ℹ [2024-03-08 02:31:44.536075]: 3.751 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_12_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_12_sim.rds
+#> ✔ [2024-03-13 10:46:06.798197]: Signature exposures collected.
+#> ✔ [2024-03-13 10:46:06.799839]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:46:06.801301]: Done.
+#> ℹ [2024-03-13 10:46:06.802744]: 3.746 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_12_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_12_sim.rds
 #> Handling sample: Sample_17
-#> ℹ [2024-03-08 02:31:44.690954]: Started.
-#> ℹ [2024-03-08 02:31:44.692962]: Checking catalog.
-#> ✔ [2024-03-08 02:31:44.694678]: Done.
-#> ℹ [2024-03-08 02:31:44.696337]: About to start bootstrap.
+#> ℹ [2024-03-13 10:46:06.975137]: Started.
+#> ℹ [2024-03-13 10:46:06.977099]: Checking catalog.
+#> ✔ [2024-03-13 10:46:06.978748]: Done.
+#> ℹ [2024-03-13 10:46:06.980349]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -4303,17 +4303,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:48.097026]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:48.098596]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:48.100011]: Done.
-#> ℹ [2024-03-08 02:31:48.101438]: 3.41 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_17_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_17_sim.rds
+#> ✔ [2024-03-13 10:46:10.521858]: Signature exposures collected.
+#> ✔ [2024-03-13 10:46:10.523606]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:46:10.525128]: Done.
+#> ℹ [2024-03-13 10:46:10.526666]: 3.551 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_17_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_17_sim.rds
 #> Handling sample: Sample_19
-#> ℹ [2024-03-08 02:31:48.260735]: Started.
-#> ℹ [2024-03-08 02:31:48.262654]: Checking catalog.
-#> ✔ [2024-03-08 02:31:48.264282]: Done.
-#> ℹ [2024-03-08 02:31:48.265784]: About to start bootstrap.
+#> ℹ [2024-03-13 10:46:10.72716]: Started.
+#> ℹ [2024-03-13 10:46:10.729144]: Checking catalog.
+#> ✔ [2024-03-13 10:46:10.730773]: Done.
+#> ℹ [2024-03-13 10:46:10.732364]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -4417,17 +4417,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:51.727399]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:51.728962]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:51.730343]: Done.
-#> ℹ [2024-03-08 02:31:51.731806]: 3.471 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_19_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_19_sim.rds
+#> ✔ [2024-03-13 10:46:14.295204]: Signature exposures collected.
+#> ✔ [2024-03-13 10:46:14.296926]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:46:14.298431]: Done.
+#> ℹ [2024-03-13 10:46:14.299999]: 3.573 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_19_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_19_sim.rds
 #> Handling sample: Sample_22
-#> ℹ [2024-03-08 02:31:51.890004]: Started.
-#> ℹ [2024-03-08 02:31:51.891966]: Checking catalog.
-#> ✔ [2024-03-08 02:31:51.893586]: Done.
-#> ℹ [2024-03-08 02:31:51.895158]: About to start bootstrap.
+#> ℹ [2024-03-13 10:46:14.475958]: Started.
+#> ℹ [2024-03-13 10:46:14.477913]: Checking catalog.
+#> ✔ [2024-03-13 10:46:14.479644]: Done.
+#> ℹ [2024-03-13 10:46:14.481263]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -4531,17 +4531,17 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:55.396132]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:55.397715]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:55.399135]: Done.
-#> ℹ [2024-03-08 02:31:55.400577]: 3.511 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_22_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_22_sim.rds
+#> ✔ [2024-03-13 10:46:18.29404]: Signature exposures collected.
+#> ✔ [2024-03-13 10:46:18.295702]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:46:18.297132]: Done.
+#> ℹ [2024-03-13 10:46:18.298594]: 3.823 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_22_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_22_sim.rds
 #> Handling sample: Sample_24
-#> ℹ [2024-03-08 02:31:55.554705]: Started.
-#> ℹ [2024-03-08 02:31:55.556512]: Checking catalog.
-#> ✔ [2024-03-08 02:31:55.557874]: Done.
-#> ℹ [2024-03-08 02:31:55.559259]: About to start bootstrap.
+#> ℹ [2024-03-13 10:46:18.47841]: Started.
+#> ℹ [2024-03-13 10:46:18.480386]: Checking catalog.
+#> ✔ [2024-03-13 10:46:18.482035]: Done.
+#> ℹ [2024-03-13 10:46:18.483627]: About to start bootstrap.
 #> → Bootstrapping 100 times.
 #> → Total 100 times, starting no.1.
 #> → Total 100 times, starting no.2.
@@ -4645,12 +4645,12 @@ 
Examples

 #> → Total 100 times, starting no.100.
 #> Bootstrap done.
 #> 
-#> ✔ [2024-03-08 02:31:59.147856]: Signature exposures collected.
-#> ✔ [2024-03-08 02:31:59.14942]: Errors and similarity collected.
-#> ✔ [2024-03-08 02:31:59.150859]: Done.
-#> ℹ [2024-03-08 02:31:59.15229]: 3.598 secs elapsed.
-#> Save expo result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_24_expo.rds
-#> Save similarity result to temp file /tmp/RtmpXZeTRm/sigminer_attribute_activity/Sample_24_sim.rds
+#> ✔ [2024-03-13 10:46:22.238601]: Signature exposures collected.
+#> ✔ [2024-03-13 10:46:22.240255]: Errors and similarity collected.
+#> ✔ [2024-03-13 10:46:22.241711]: Done.
+#> ℹ [2024-03-13 10:46:22.243196]: 3.765 secs elapsed.
+#> Save expo result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_24_expo.rds
+#> Save similarity result to temp file /tmp/RtmpT86DiN/sigminer_attribute_activity/Sample_24_sim.rds
 #> 
 #> Reading result files...
 #> Clean cache files when exits.
diff --git a/reference/get_group_comparison.html b/reference/get_group_comparison.html
index 7d64cf50..855108cc 100644
--- a/reference/get_group_comparison.html
+++ b/reference/get_group_comparison.html
@@ -138,19 +138,19 @@ 
Examples

 
 # Assign samples to clusters
 groups <- get_groups(sig, method = "k-means")
-#> ℹ [2024-03-08 02:32:06.604791]: Started.
-#> ✔ [2024-03-08 02:32:06.606448]: 'Signature' object detected.
-#> ℹ [2024-03-08 02:32:06.611614]: Running k-means with 2 clusters...
-#> ℹ [2024-03-08 02:32:06.615206]: Generating a table of group and signature contribution (stored in 'map_table' attr):
+#> ℹ [2024-03-13 10:46:29.835536]: Started.
+#> ✔ [2024-03-13 10:46:29.837225]: 'Signature' object detected.
+#> ℹ [2024-03-13 10:46:29.842497]: Running k-means with 2 clusters...
+#> ℹ [2024-03-13 10:46:29.85173]: Generating a table of group and signature contribution (stored in 'map_table' attr):
 #>        Sig1      Sig2
 #> 1 0.2097559 0.7901116
 #> 2 0.8964984 0.1035016
-#> ℹ [2024-03-08 02:32:06.616614]: Assigning a group to a signature with the maximum fraction...
-#> ℹ [2024-03-08 02:32:06.619962]: Summarizing...
+#> ℹ [2024-03-13 10:46:29.854921]: Assigning a group to a signature with the maximum fraction...
+#> ℹ [2024-03-13 10:46:29.858319]: Summarizing...
 #> 	group #1: 2 samples with Sig2 enriched.
 #> 	group #2: 8 samples with Sig1 enriched.
-#> ! [2024-03-08 02:32:06.621872]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
-#> ℹ [2024-03-08 02:32:06.623384]: 0.019 secs elapsed.
+#> ! [2024-03-13 10:46:29.860314]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
+#> ℹ [2024-03-13 10:46:29.861816]: 0.026 secs elapsed.
 
 set.seed(1234)
 
diff --git a/reference/get_groups.html b/reference/get_groups.html
index 56569859..bbb30b20 100644
--- a/reference/get_groups.html
+++ b/reference/get_groups.html
@@ -151,25 +151,25 @@ 
Examples

 #> 
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 #> System time:
 #>    user  system elapsed 
-#>   4.631   0.008   4.642 
+#>   4.790   0.000   4.789 
 
 # Methods 'consensus' and 'samples' are from NMF::predict()
 g1 <- get_groups(sig, method = "consensus", match_consensus = TRUE)
-#> ℹ [2024-03-08 02:32:12.089741]: Started.
-#> ✔ [2024-03-08 02:32:12.091405]: 'Signature' object detected.
-#> ℹ [2024-03-08 02:32:12.09275]: Obtaining clusters from the hierarchical clustering of the consensus matrix...
-#> ℹ [2024-03-08 02:32:12.110096]: Finding the dominant signature of each group...
+#> ℹ [2024-03-13 10:46:35.554339]: Started.
+#> ✔ [2024-03-13 10:46:35.556152]: 'Signature' object detected.
+#> ℹ [2024-03-13 10:46:35.557788]: Obtaining clusters from the hierarchical clustering of the consensus matrix...
+#> ℹ [2024-03-13 10:46:35.5774]: Finding the dominant signature of each group...
 #> => Generating a table of group and dominant signature:
 #>    
 #>     Sig1 Sig2
 #>   1    0    2
 #>   2    8    0
 #> => Assigning a group to a signature with the maxium fraction (stored in 'map_table' attr)...
-#> ℹ [2024-03-08 02:32:12.125983]: Summarizing...
+#> ℹ [2024-03-13 10:46:35.59536]: Summarizing...
 #> 	group #1: 2 samples with Sig2 enriched.
 #> 	group #2: 8 samples with Sig1 enriched.
-#> ! [2024-03-08 02:32:12.127929]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
-#> ℹ [2024-03-08 02:32:12.129322]: 0.04 secs elapsed.
+#> ! [2024-03-13 10:46:35.597567]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
+#> ℹ [2024-03-13 10:46:35.599155]: 0.045 secs elapsed.
 g1
 #>                           sample  group silhouette_width enrich_sig
 #>                           <char> <char>            <num>     <char>
@@ -184,21 +184,21 @@ 
Examples

 #>  9: TCGA-06-0644-01A-02D-0310-01      2            1.000       Sig1
 #> 10: TCGA-19-2621-01B-01D-0911-01      2            0.889       Sig1
 g2 <- get_groups(sig, method = "samples")
-#> ℹ [2024-03-08 02:32:12.133194]: Started.
-#> ✔ [2024-03-08 02:32:12.134541]: 'Signature' object detected.
-#> ℹ [2024-03-08 02:32:12.135909]: Obtaining clusters by the contribution of signature to each sample...
-#> ℹ [2024-03-08 02:32:12.138719]: Finding the dominant signature of each group...
+#> ℹ [2024-03-13 10:46:35.603586]: Started.
+#> ✔ [2024-03-13 10:46:35.605161]: 'Signature' object detected.
+#> ℹ [2024-03-13 10:46:35.606695]: Obtaining clusters by the contribution of signature to each sample...
+#> ℹ [2024-03-13 10:46:35.609896]: Finding the dominant signature of each group...
 #> => Generating a table of group and dominant signature:
 #>    
 #>     Sig1 Sig2
 #>   1    0    2
 #>   2    8    0
 #> => Assigning a group to a signature with the maxium fraction (stored in 'map_table' attr)...
-#> ℹ [2024-03-08 02:32:12.153297]: Summarizing...
+#> ℹ [2024-03-13 10:46:35.625684]: Summarizing...
 #> 	group #1: 2 samples with Sig2 enriched.
 #> 	group #2: 8 samples with Sig1 enriched.
-#> ! [2024-03-08 02:32:12.155224]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
-#> ℹ [2024-03-08 02:32:12.156627]: 0.023 secs elapsed.
+#> ! [2024-03-13 10:46:35.627838]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
+#> ℹ [2024-03-13 10:46:35.629398]: 0.026 secs elapsed.
 g2
 #>                           sample  group silhouette_width  prob enrich_sig
 #>                           <char> <char>            <num> <num>     <char>
@@ -215,19 +215,19 @@ 
Examples

 
 # Use k-means clustering
 g3 <- get_groups(sig, method = "k-means")
-#> ℹ [2024-03-08 02:32:12.160769]: Started.
-#> ✔ [2024-03-08 02:32:12.162225]: 'Signature' object detected.
-#> ℹ [2024-03-08 02:32:12.165922]: Running k-means with 2 clusters...
-#> ℹ [2024-03-08 02:32:12.168246]: Generating a table of group and signature contribution (stored in 'map_table' attr):
+#> ℹ [2024-03-13 10:46:35.633968]: Started.
+#> ✔ [2024-03-13 10:46:35.635537]: 'Signature' object detected.
+#> ℹ [2024-03-13 10:46:35.639543]: Running k-means with 2 clusters...
+#> ℹ [2024-03-13 10:46:35.641938]: Generating a table of group and signature contribution (stored in 'map_table' attr):
 #>        Sig1      Sig2
 #> 1 0.2097559 0.7901116
 #> 2 0.8964984 0.1035016
-#> ℹ [2024-03-08 02:32:12.169668]: Assigning a group to a signature with the maximum fraction...
-#> ℹ [2024-03-08 02:32:12.173079]: Summarizing...
+#> ℹ [2024-03-13 10:46:35.643506]: Assigning a group to a signature with the maximum fraction...
+#> ℹ [2024-03-13 10:46:35.647204]: Summarizing...
 #> 	group #1: 2 samples with Sig2 enriched.
 #> 	group #2: 8 samples with Sig1 enriched.
-#> ! [2024-03-08 02:32:12.174906]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
-#> ℹ [2024-03-08 02:32:12.1763]: 0.015 secs elapsed.
+#> ! [2024-03-13 10:46:35.64922]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
+#> ℹ [2024-03-13 10:46:35.650689]: 0.017 secs elapsed.
 g3
 #> Key: <group>
 #>                           sample  group silhouette_width enrich_sig
diff --git a/reference/get_pLOH_score.html b/reference/get_pLOH_score.html
index 374e35fb..73f6730c 100644
--- a/reference/get_pLOH_score.html
+++ b/reference/get_pLOH_score.html
@@ -112,36 +112,36 @@ 
Examples

   seg_cols = c("chromosome", "start", "end", "segVal"),
   genome_measure = "wg", complement = TRUE, add_loh = TRUE
 )
-#> ℹ [2024-03-08 02:32:12.521385]: Started.
-#> ℹ [2024-03-08 02:32:12.523124]: Genome build  : hg19.
-#> ℹ [2024-03-08 02:32:12.524469]: Genome measure: wg.
-#> ℹ [2024-03-08 02:32:12.525781]: When add_loh is TRUE, use_all is forced to TRUE.
+#> ℹ [2024-03-13 10:46:36.021596]: Started.
+#> ℹ [2024-03-13 10:46:36.023285]: Genome build  : hg19.
+#> ℹ [2024-03-13 10:46:36.024638]: Genome measure: wg.
+#> ℹ [2024-03-13 10:46:36.025951]: When add_loh is TRUE, use_all is forced to TRUE.
 #> Please drop columns you don't want to keep before reading.
-#> ✔ [2024-03-08 02:32:12.529832]: Chromosome size database for build obtained.
-#> ℹ [2024-03-08 02:32:12.531242]: Reading input.
-#> ✔ [2024-03-08 02:32:12.532586]: A data frame as input detected.
-#> ✔ [2024-03-08 02:32:12.533983]: Column names checked.
-#> ✔ [2024-03-08 02:32:12.535395]: Column order set.
-#> ✔ [2024-03-08 02:32:12.538193]: Chromosomes unified.
-#> ✔ [2024-03-08 02:32:12.551173]: Value 2 (normal copy) filled to uncalled chromosomes.
-#> ✔ [2024-03-08 02:32:12.555232]: Data imported.
-#> ℹ [2024-03-08 02:32:12.556619]: Segments info:
-#> ℹ [2024-03-08 02:32:12.557959]:     Keep - 477
-#> ℹ [2024-03-08 02:32:12.559325]:     Drop - 0
-#> ✔ [2024-03-08 02:32:12.561141]: Segments sorted.
-#> ℹ [2024-03-08 02:32:12.562491]: Adding LOH labels...
-#> ℹ [2024-03-08 02:32:12.564355]: Joining adjacent segments with same copy number value. Be patient...
-#> ✔ [2024-03-08 02:32:12.67294]: 410 segments left after joining.
-#> ✔ [2024-03-08 02:32:12.674948]: Segmental table cleaned.
-#> ℹ [2024-03-08 02:32:12.676298]: Annotating.
-#> ✔ [2024-03-08 02:32:12.689319]: Annotation done.
-#> ℹ [2024-03-08 02:32:12.690717]: Summarizing per sample.
-#> ✔ [2024-03-08 02:32:12.703563]: Summarized.
-#> ℹ [2024-03-08 02:32:12.705024]: Generating CopyNumber object.
-#> ✔ [2024-03-08 02:32:12.706943]: Generated.
-#> ℹ [2024-03-08 02:32:12.708302]: Validating object.
-#> ✔ [2024-03-08 02:32:12.709707]: Done.
-#> ℹ [2024-03-08 02:32:12.711103]: 0.19 secs elapsed.
+#> ✔ [2024-03-13 10:46:36.030026]: Chromosome size database for build obtained.
+#> ℹ [2024-03-13 10:46:36.031436]: Reading input.
+#> ✔ [2024-03-13 10:46:36.032809]: A data frame as input detected.
+#> ✔ [2024-03-13 10:46:36.03425]: Column names checked.
+#> ✔ [2024-03-13 10:46:36.035709]: Column order set.
+#> ✔ [2024-03-13 10:46:36.038584]: Chromosomes unified.
+#> ✔ [2024-03-13 10:46:36.05189]: Value 2 (normal copy) filled to uncalled chromosomes.
+#> ✔ [2024-03-13 10:46:36.056146]: Data imported.
+#> ℹ [2024-03-13 10:46:36.05759]: Segments info:
+#> ℹ [2024-03-13 10:46:36.058942]:     Keep - 477
+#> ℹ [2024-03-13 10:46:36.060323]:     Drop - 0
+#> ✔ [2024-03-13 10:46:36.062133]: Segments sorted.
+#> ℹ [2024-03-13 10:46:36.063533]: Adding LOH labels...
+#> ℹ [2024-03-13 10:46:36.065402]: Joining adjacent segments with same copy number value. Be patient...
+#> ✔ [2024-03-13 10:46:36.17035]: 410 segments left after joining.
+#> ✔ [2024-03-13 10:46:36.177701]: Segmental table cleaned.
+#> ℹ [2024-03-13 10:46:36.179195]: Annotating.
+#> ✔ [2024-03-13 10:46:36.1924]: Annotation done.
+#> ℹ [2024-03-13 10:46:36.193974]: Summarizing per sample.
+#> ✔ [2024-03-13 10:46:36.207344]: Summarized.
+#> ℹ [2024-03-13 10:46:36.208894]: Generating CopyNumber object.
+#> ✔ [2024-03-13 10:46:36.210773]: Generated.
+#> ℹ [2024-03-13 10:46:36.212134]: Validating object.
+#> ✔ [2024-03-13 10:46:36.213554]: Done.
+#> ℹ [2024-03-13 10:46:36.214929]: 0.193 secs elapsed.
 
 df <- get_pLOH_score(cn)
 df
diff --git a/reference/read_copynumber.html b/reference/read_copynumber.html
index 50c90f55..d20f3b94 100644
--- a/reference/read_copynumber.html
+++ b/reference/read_copynumber.html
@@ -206,32 +206,32 @@ 
Examples

   seg_cols = c("chromosome", "start", "end", "segVal"),
   genome_build = "hg19", complement = FALSE
 )
-#> ℹ [2024-03-08 02:32:16.906099]: Started.
-#> ℹ [2024-03-08 02:32:16.907814]: Genome build  : hg19.
-#> ℹ [2024-03-08 02:32:16.909132]: Genome measure: called.
-#> ✔ [2024-03-08 02:32:16.913171]: Chromosome size database for build obtained.
-#> ℹ [2024-03-08 02:32:16.914541]: Reading input.
-#> ✔ [2024-03-08 02:32:16.91591]: A data frame as input detected.
-#> ✔ [2024-03-08 02:32:16.917337]: Column names checked.
-#> ✔ [2024-03-08 02:32:16.918722]: Column order set.
-#> ✔ [2024-03-08 02:32:16.921685]: Chromosomes unified.
-#> ✔ [2024-03-08 02:32:16.925401]: Data imported.
-#> ℹ [2024-03-08 02:32:16.926797]: Segments info:
-#> ℹ [2024-03-08 02:32:16.928223]:     Keep - 467
-#> ℹ [2024-03-08 02:32:16.929597]:     Drop - 0
-#> ✔ [2024-03-08 02:32:16.931243]: Segments sorted.
-#> ℹ [2024-03-08 02:32:16.932568]: Joining adjacent segments with same copy number value. Be patient...
-#> ✔ [2024-03-08 02:32:17.014903]: 400 segments left after joining.
-#> ✔ [2024-03-08 02:32:17.016913]: Segmental table cleaned.
-#> ℹ [2024-03-08 02:32:17.018282]: Annotating.
-#> ✔ [2024-03-08 02:32:17.031497]: Annotation done.
-#> ℹ [2024-03-08 02:32:17.032922]: Summarizing per sample.
-#> ✔ [2024-03-08 02:32:17.042883]: Summarized.
-#> ℹ [2024-03-08 02:32:17.044281]: Generating CopyNumber object.
-#> ✔ [2024-03-08 02:32:17.045869]: Generated.
-#> ℹ [2024-03-08 02:32:17.047239]: Validating object.
-#> ✔ [2024-03-08 02:32:17.048635]: Done.
-#> ℹ [2024-03-08 02:32:17.050026]: 0.144 secs elapsed.
+#> ℹ [2024-03-13 10:46:40.615923]: Started.
+#> ℹ [2024-03-13 10:46:40.617606]: Genome build  : hg19.
+#> ℹ [2024-03-13 10:46:40.618965]: Genome measure: called.
+#> ✔ [2024-03-13 10:46:40.623153]: Chromosome size database for build obtained.
+#> ℹ [2024-03-13 10:46:40.624629]: Reading input.
+#> ✔ [2024-03-13 10:46:40.626049]: A data frame as input detected.
+#> ✔ [2024-03-13 10:46:40.627542]: Column names checked.
+#> ✔ [2024-03-13 10:46:40.629049]: Column order set.
+#> ✔ [2024-03-13 10:46:40.631985]: Chromosomes unified.
+#> ✔ [2024-03-13 10:46:40.635806]: Data imported.
+#> ℹ [2024-03-13 10:46:40.637217]: Segments info:
+#> ℹ [2024-03-13 10:46:40.638582]:     Keep - 467
+#> ℹ [2024-03-13 10:46:40.639965]:     Drop - 0
+#> ✔ [2024-03-13 10:46:40.641627]: Segments sorted.
+#> ℹ [2024-03-13 10:46:40.642978]: Joining adjacent segments with same copy number value. Be patient...
+#> ✔ [2024-03-13 10:46:40.728295]: 400 segments left after joining.
+#> ✔ [2024-03-13 10:46:40.730196]: Segmental table cleaned.
+#> ℹ [2024-03-13 10:46:40.731591]: Annotating.
+#> ✔ [2024-03-13 10:46:40.744683]: Annotation done.
+#> ℹ [2024-03-13 10:46:40.746104]: Summarizing per sample.
+#> ✔ [2024-03-13 10:46:40.756001]: Summarized.
+#> ℹ [2024-03-13 10:46:40.757412]: Generating CopyNumber object.
+#> ✔ [2024-03-13 10:46:40.758999]: Generated.
+#> ℹ [2024-03-13 10:46:40.760376]: Validating object.
+#> ✔ [2024-03-13 10:46:40.761738]: Done.
+#> ℹ [2024-03-13 10:46:40.763145]: 0.147 secs elapsed.
 cn
 #> An object of class CopyNumber 
 #> =============================
@@ -268,73 +268,73 @@ 
Examples

   seg_cols = c("chromosome", "start", "end", "segVal"),
   genome_measure = "wg", complement = TRUE, add_loh = TRUE
 )
-#> ℹ [2024-03-08 02:32:17.065503]: Started.
-#> ℹ [2024-03-08 02:32:17.066971]: Genome build  : hg19.
-#> ℹ [2024-03-08 02:32:17.068347]: Genome measure: wg.
-#> ℹ [2024-03-08 02:32:17.069707]: When add_loh is TRUE, use_all is forced to TRUE.
+#> ℹ [2024-03-13 10:46:40.778973]: Started.
+#> ℹ [2024-03-13 10:46:40.780502]: Genome build  : hg19.
+#> ℹ [2024-03-13 10:46:40.781865]: Genome measure: wg.
+#> ℹ [2024-03-13 10:46:40.78319]: When add_loh is TRUE, use_all is forced to TRUE.
 #> Please drop columns you don't want to keep before reading.
-#> ✔ [2024-03-08 02:32:17.079928]: Chromosome size database for build obtained.
-#> ℹ [2024-03-08 02:32:17.081365]: Reading input.
-#> ✔ [2024-03-08 02:32:17.082739]: A data frame as input detected.
-#> ✔ [2024-03-08 02:32:17.084196]: Column names checked.
-#> ✔ [2024-03-08 02:32:17.085624]: Column order set.
-#> ✔ [2024-03-08 02:32:17.088461]: Chromosomes unified.
-#> ✔ [2024-03-08 02:32:17.101281]: Value 2 (normal copy) filled to uncalled chromosomes.
-#> ✔ [2024-03-08 02:32:17.104909]: Data imported.
-#> ℹ [2024-03-08 02:32:17.106321]: Segments info:
-#> ℹ [2024-03-08 02:32:17.107697]:     Keep - 477
-#> ℹ [2024-03-08 02:32:17.109013]:     Drop - 0
-#> ✔ [2024-03-08 02:32:17.110675]: Segments sorted.
-#> ℹ [2024-03-08 02:32:17.11204]: Adding LOH labels...
-#> ℹ [2024-03-08 02:32:17.113837]: Joining adjacent segments with same copy number value. Be patient...
-#> ✔ [2024-03-08 02:32:17.246777]: 410 segments left after joining.
-#> ✔ [2024-03-08 02:32:17.248788]: Segmental table cleaned.
-#> ℹ [2024-03-08 02:32:17.25017]: Annotating.
-#> ✔ [2024-03-08 02:32:17.26368]: Annotation done.
-#> ℹ [2024-03-08 02:32:17.265073]: Summarizing per sample.
-#> ✔ [2024-03-08 02:32:17.277394]: Summarized.
-#> ℹ [2024-03-08 02:32:17.278769]: Generating CopyNumber object.
-#> ✔ [2024-03-08 02:32:17.280374]: Generated.
-#> ℹ [2024-03-08 02:32:17.281697]: Validating object.
-#> ✔ [2024-03-08 02:32:17.283057]: Done.
-#> ℹ [2024-03-08 02:32:17.284443]: 0.219 secs elapsed.
+#> ✔ [2024-03-13 10:46:40.786907]: Chromosome size database for build obtained.
+#> ℹ [2024-03-13 10:46:40.788351]: Reading input.
+#> ✔ [2024-03-13 10:46:40.789747]: A data frame as input detected.
+#> ✔ [2024-03-13 10:46:40.791192]: Column names checked.
+#> ✔ [2024-03-13 10:46:40.792676]: Column order set.
+#> ✔ [2024-03-13 10:46:40.79571]: Chromosomes unified.
+#> ✔ [2024-03-13 10:46:40.808891]: Value 2 (normal copy) filled to uncalled chromosomes.
+#> ✔ [2024-03-13 10:46:40.812646]: Data imported.
+#> ℹ [2024-03-13 10:46:40.814126]: Segments info:
+#> ℹ [2024-03-13 10:46:40.815526]:     Keep - 477
+#> ℹ [2024-03-13 10:46:40.816952]:     Drop - 0
+#> ✔ [2024-03-13 10:46:40.818662]: Segments sorted.
+#> ℹ [2024-03-13 10:46:40.820101]: Adding LOH labels...
+#> ℹ [2024-03-13 10:46:40.822013]: Joining adjacent segments with same copy number value. Be patient...
+#> ✔ [2024-03-13 10:46:40.931891]: 410 segments left after joining.
+#> ✔ [2024-03-13 10:46:40.933873]: Segmental table cleaned.
+#> ℹ [2024-03-13 10:46:40.935365]: Annotating.
+#> ✔ [2024-03-13 10:46:40.949005]: Annotation done.
+#> ℹ [2024-03-13 10:46:40.9505]: Summarizing per sample.
+#> ✔ [2024-03-13 10:46:40.963472]: Summarized.
+#> ℹ [2024-03-13 10:46:40.965031]: Generating CopyNumber object.
+#> ✔ [2024-03-13 10:46:40.966737]: Generated.
+#> ℹ [2024-03-13 10:46:40.968155]: Validating object.
+#> ✔ [2024-03-13 10:46:40.96953]: Done.
+#> ℹ [2024-03-13 10:46:40.970948]: 0.192 secs elapsed.
 # Use tally method "S" (Steele et al.)
 tally_s <- sig_tally(cn, method = "S")
-#> ℹ [2024-03-08 02:32:17.286712]: Started.
-#> ℹ [2024-03-08 02:32:17.290398]: When you use method 'S', please make sure you have set 'join_adj_seg' to FALSE and 'add_loh' to TRUE in 'read_copynumber() in the previous step!
-#> ✔ [2024-03-08 02:32:17.303504]: Matrix generated.
-#> ℹ [2024-03-08 02:32:17.305003]: 0.018 secs elapsed.
+#> ℹ [2024-03-13 10:46:40.973325]: Started.
+#> ℹ [2024-03-13 10:46:40.977145]: When you use method 'S', please make sure you have set 'join_adj_seg' to FALSE and 'add_loh' to TRUE in 'read_copynumber() in the previous step!
+#> ✔ [2024-03-13 10:46:40.990102]: Matrix generated.
+#> ℹ [2024-03-13 10:46:40.991696]: 0.018 secs elapsed.
 
 tab_file <- system.file("extdata", "metastatic_tumor.segtab.txt",
   package = "sigminer", mustWork = TRUE
 )
 cn2 <- read_copynumber(tab_file)
-#> ℹ [2024-03-08 02:32:17.308259]: Started.
-#> ℹ [2024-03-08 02:32:17.309667]: Genome build  : hg19.
-#> ℹ [2024-03-08 02:32:17.31106]: Genome measure: called.
-#> ✔ [2024-03-08 02:32:17.315138]: Chromosome size database for build obtained.
-#> ℹ [2024-03-08 02:32:17.316509]: Reading input.
-#> ✔ [2024-03-08 02:32:17.317841]: A file as input detected.
-#> ✔ [2024-03-08 02:32:17.320016]: Column names checked.
-#> ✔ [2024-03-08 02:32:17.321493]: Column order set.
-#> ✔ [2024-03-08 02:32:17.324168]: Chromosomes unified.
-#> ✔ [2024-03-08 02:32:17.327838]: Data imported.
-#> ℹ [2024-03-08 02:32:17.329223]: Segments info:
-#> ℹ [2024-03-08 02:32:17.33066]:     Keep - 201
-#> ℹ [2024-03-08 02:32:17.332542]:     Drop - 0
-#> ✔ [2024-03-08 02:32:17.335497]: Segments sorted.
-#> ℹ [2024-03-08 02:32:17.337895]: Joining adjacent segments with same copy number value. Be patient...
-#> ✔ [2024-03-08 02:32:17.359381]: 180 segments left after joining.
-#> ✔ [2024-03-08 02:32:17.361424]: Segmental table cleaned.
-#> ℹ [2024-03-08 02:32:17.36288]: Annotating.
-#> ✔ [2024-03-08 02:32:17.384777]: Annotation done.
-#> ℹ [2024-03-08 02:32:17.386441]: Summarizing per sample.
-#> ✔ [2024-03-08 02:32:17.396447]: Summarized.
-#> ℹ [2024-03-08 02:32:17.39788]: Generating CopyNumber object.
-#> ✔ [2024-03-08 02:32:17.399525]: Generated.
-#> ℹ [2024-03-08 02:32:17.400868]: Validating object.
-#> ✔ [2024-03-08 02:32:17.402203]: Done.
-#> ℹ [2024-03-08 02:32:17.403597]: 0.095 secs elapsed.
+#> ℹ [2024-03-13 10:46:40.994992]: Started.
+#> ℹ [2024-03-13 10:46:40.996476]: Genome build  : hg19.
+#> ℹ [2024-03-13 10:46:40.997838]: Genome measure: called.
+#> ✔ [2024-03-13 10:46:41.009108]: Chromosome size database for build obtained.
+#> ℹ [2024-03-13 10:46:41.010733]: Reading input.
+#> ✔ [2024-03-13 10:46:41.012132]: A file as input detected.
+#> ✔ [2024-03-13 10:46:41.014337]: Column names checked.
+#> ✔ [2024-03-13 10:46:41.015902]: Column order set.
+#> ✔ [2024-03-13 10:46:41.018509]: Chromosomes unified.
+#> ✔ [2024-03-13 10:46:41.022197]: Data imported.
+#> ℹ [2024-03-13 10:46:41.023641]: Segments info:
+#> ℹ [2024-03-13 10:46:41.024997]:     Keep - 201
+#> ℹ [2024-03-13 10:46:41.026328]:     Drop - 0
+#> ✔ [2024-03-13 10:46:41.028004]: Segments sorted.
+#> ℹ [2024-03-13 10:46:41.02934]: Joining adjacent segments with same copy number value. Be patient...
+#> ✔ [2024-03-13 10:46:41.045211]: 180 segments left after joining.
+#> ✔ [2024-03-13 10:46:41.046876]: Segmental table cleaned.
+#> ℹ [2024-03-13 10:46:41.048282]: Annotating.
+#> ✔ [2024-03-13 10:46:41.061738]: Annotation done.
+#> ℹ [2024-03-13 10:46:41.063629]: Summarizing per sample.
+#> ✔ [2024-03-13 10:46:41.074651]: Summarized.
+#> ℹ [2024-03-13 10:46:41.076296]: Generating CopyNumber object.
+#> ✔ [2024-03-13 10:46:41.078102]: Generated.
+#> ℹ [2024-03-13 10:46:41.079652]: Validating object.
+#> ✔ [2024-03-13 10:46:41.081135]: Done.
+#> ℹ [2024-03-13 10:46:41.082609]: 0.088 secs elapsed.
 cn2
 #> An object of class CopyNumber 
 #> =============================
diff --git a/reference/read_maf.html b/reference/read_maf.html
index 6e1356f7..75c9b5af 100644
--- a/reference/read_maf.html
+++ b/reference/read_maf.html
@@ -153,7 +153,7 @@ 
Examples

 #> -Summarizing
 #> -Processing clinical data
 #> --Missing clinical data
-#> -Finished in 0.211s elapsed (0.247s cpu) 
+#> -Finished in 0.214s elapsed (0.252s cpu) 
 #> Please note that the generated MAF object is designed for mutational signature analysis, not recommended for Maftools analysis!
 #> An object of class  MAF 
 #>            ID summary  Mean Median
diff --git a/reference/read_vcf.html b/reference/read_vcf.html
index 2dcb5d94..beb07429 100644
--- a/reference/read_vcf.html
+++ b/reference/read_vcf.html
@@ -127,7 +127,7 @@ 
Examples

 #> -Summarizing
 #> -Processing clinical data
 #> --Missing clinical data
-#> -Finished in 0.025s elapsed (0.039s cpu) 
+#> -Finished in 0.024s elapsed (0.039s cpu) 
 maf <- read_vcf(vcfs, keep_only_pass = TRUE)
 #> Reading file(s): /home/runner/work/_temp/Library/sigminer/extdata/test1.vcf, /home/runner/work/_temp/Library/sigminer/extdata/test2.vcf, /home/runner/work/_temp/Library/sigminer/extdata/test3.vcf
 #> It seems /home/runner/work/_temp/Library/sigminer/extdata/test2.vcf has no normal VCF header, try parsing without header.
diff --git a/reference/read_xena_variants.html b/reference/read_xena_variants.html
index 595490f8..c017e121 100644
--- a/reference/read_xena_variants.html
+++ b/reference/read_xena_variants.html
@@ -115,12 +115,13 @@ 
Examples

 #>     samples
 #> The hiplot server may down, we will not use it for now.
 #> This will check url status, please be patient.
-#> All downloaded files will under directory /tmp/RtmpXZeTRm.
+#> All downloaded files will under directory /tmp/RtmpT86DiN.
 #> The 'trans_slash' option is FALSE, keep same directory structure as Xena.
 #> Creating directories for datasets...
 #> Downloading mc3/ACC_mc3.txt.gz
-#> ℹ [2024-03-08 02:32:25.216767]: Started.
-#> ℹ [2024-03-08 02:32:31.204548]: We would assume you marked all variants' position in + strand.
+#> ℹ [2024-03-13 10:46:50.128063]: Started.
+#> Warning: replacing previous import ‘S4Arrays::makeNindexFromArrayViewport’ by ‘DelayedArray::makeNindexFromArrayViewport’ when loading ‘SummarizedExperiment’
+#> ℹ [2024-03-13 10:46:59.437203]: We would assume you marked all variants' position in + strand.
 #> 
 #> Attaching package: ‘S4Vectors’
 #> The following object is masked from ‘package:NMF’:
@@ -155,26 +156,26 @@ 
Examples

 #> The following object is masked from ‘package:BiocIO’:
 #> 
 #>     FileForFormat
-#> ✔ [2024-03-08 02:32:32.025742]: Reference genome loaded.
-#> ✔ [2024-03-08 02:32:32.0329]: Variants from MAF object queried.
-#> ✔ [2024-03-08 02:32:32.038651]: Chromosome names checked.
-#> ✔ [2024-03-08 02:32:32.048566]: Sex chromosomes properly handled.
-#> ✔ [2024-03-08 02:32:32.050876]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept.
-#> ✔ [2024-03-08 02:32:32.073653]: Variant start and end position checked.
-#> ✔ [2024-03-08 02:32:32.078166]: Variant data for matrix generation preprocessed.
-#> ℹ [2024-03-08 02:32:32.080603]: SBS matrix generation - start.
-#> ℹ [2024-03-08 02:32:32.083334]: Extracting 5' and 3' adjacent bases.
-#> ℹ [2024-03-08 02:32:32.603156]: Extracting +/- 20bp around mutated bases for background C>T estimation.
-#> ℹ [2024-03-08 02:32:33.11546]: Estimating APOBEC enrichment scores.
-#> ℹ [2024-03-08 02:32:33.117399]: Performing one-way Fisher's test for APOBEC enrichment.
-#> ✔ [2024-03-08 02:32:33.169402]: APOBEC related mutations are enriched in 19.565% of samples (APOBEC enrichment score > 2; 18 of 92 samples)
-#> ℹ [2024-03-08 02:32:33.1731]: Creating SBS sample-by-component matrices.
-#> ✔ [2024-03-08 02:32:33.178334]: SBS-6 matrix created.
-#> ✔ [2024-03-08 02:32:33.183791]: SBS-96 matrix created.
-#> ✔ [2024-03-08 02:32:33.198959]: SBS-1536 matrix created.
-#> ℹ [2024-03-08 02:32:33.200543]: Return SBS-96 as major matrix.
-#> ✔ [2024-03-08 02:32:33.202854]: Done.
-#> ℹ [2024-03-08 02:32:33.204284]: 7.987 secs elapsed.
+#> ✔ [2024-03-13 10:46:59.558154]: Reference genome loaded.
+#> ✔ [2024-03-13 10:46:59.568908]: Variants from MAF object queried.
+#> ✔ [2024-03-13 10:46:59.575953]: Chromosome names checked.
+#> ✔ [2024-03-13 10:46:59.587384]: Sex chromosomes properly handled.
+#> ✔ [2024-03-13 10:46:59.590183]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept.
+#> ✔ [2024-03-13 10:46:59.613479]: Variant start and end position checked.
+#> ✔ [2024-03-13 10:46:59.619054]: Variant data for matrix generation preprocessed.
+#> ℹ [2024-03-13 10:46:59.621973]: SBS matrix generation - start.
+#> ℹ [2024-03-13 10:46:59.625231]: Extracting 5' and 3' adjacent bases.
+#> ℹ [2024-03-13 10:47:00.208662]: Extracting +/- 20bp around mutated bases for background C>T estimation.
+#> ℹ [2024-03-13 10:47:00.693055]: Estimating APOBEC enrichment scores.
+#> ℹ [2024-03-13 10:47:00.695056]: Performing one-way Fisher's test for APOBEC enrichment.
+#> ✔ [2024-03-13 10:47:00.747178]: APOBEC related mutations are enriched in 19.565% of samples (APOBEC enrichment score > 2; 18 of 92 samples)
+#> ℹ [2024-03-13 10:47:00.750856]: Creating SBS sample-by-component matrices.
+#> ✔ [2024-03-13 10:47:00.756007]: SBS-6 matrix created.
+#> ✔ [2024-03-13 10:47:00.761486]: SBS-96 matrix created.
+#> ✔ [2024-03-13 10:47:00.776806]: SBS-1536 matrix created.
+#> ℹ [2024-03-13 10:47:00.778538]: Return SBS-96 as major matrix.
+#> ✔ [2024-03-13 10:47:00.780903]: Done.
+#> ℹ [2024-03-13 10:47:00.782426]: 10.654 secs elapsed.
 #> $nmf_matrix
 #>                 A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T
 #> TCGA-OR-A5J1-01       0       0       0       0       1       1       0       1
diff --git a/reference/show_group_comparison.html b/reference/show_group_comparison.html
index adf18ecd..0d412a88 100644
--- a/reference/show_group_comparison.html
+++ b/reference/show_group_comparison.html
@@ -193,19 +193,19 @@ 
Examples

 
 # Assign samples to clusters
 groups <- get_groups(sig, method = "k-means")
-#> ℹ [2024-03-08 02:33:49.7457]: Started.
-#> ✔ [2024-03-08 02:33:49.747522]: 'Signature' object detected.
-#> ℹ [2024-03-08 02:33:49.752067]: Running k-means with 2 clusters...
-#> ℹ [2024-03-08 02:33:49.754484]: Generating a table of group and signature contribution (stored in 'map_table' attr):
+#> ℹ [2024-03-13 10:48:16.773885]: Started.
+#> ✔ [2024-03-13 10:48:16.775684]: 'Signature' object detected.
+#> ℹ [2024-03-13 10:48:16.780108]: Running k-means with 2 clusters...
+#> ℹ [2024-03-13 10:48:16.782395]: Generating a table of group and signature contribution (stored in 'map_table' attr):
 #>        Sig1      Sig2
 #> 1 0.2097559 0.7901116
 #> 2 0.8964984 0.1035016
-#> ℹ [2024-03-08 02:33:49.75602]: Assigning a group to a signature with the maximum fraction...
-#> ℹ [2024-03-08 02:33:49.759632]: Summarizing...
+#> ℹ [2024-03-13 10:48:16.783921]: Assigning a group to a signature with the maximum fraction...
+#> ℹ [2024-03-13 10:48:16.787456]: Summarizing...
 #> 	group #1: 2 samples with Sig2 enriched.
 #> 	group #2: 8 samples with Sig1 enriched.
-#> ! [2024-03-08 02:33:49.76152]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
-#> ℹ [2024-03-08 02:33:49.763034]: 0.017 secs elapsed.
+#> ! [2024-03-13 10:48:16.789341]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary).
+#> ℹ [2024-03-13 10:48:16.790794]: 0.017 secs elapsed.
 
 set.seed(1234)
 
diff --git a/reference/show_group_enrichment.html b/reference/show_group_enrichment.html
index d05582c5..57b932c6 100644
--- a/reference/show_group_enrichment.html
+++ b/reference/show_group_enrichment.html
@@ -81,6 +81,7 @@ 
Show Group Enrichment Result

   fill_scale = scale_fill_gradient2(low = "#08A76B", mid = "white", high = "red",
     midpoint = ifelse(fill_by_p_value, 0, 1)),
   cluster_row = FALSE,
+  cluster_col = FALSE,
   ...
 )
@@ -136,8 +137,8 @@

Arguments

set color for continuous values.

-
cluster_row
-

if TRUE, cluster rows with Hierarchical Clustering ('complete' method).

+
cluster_row, cluster_col
+

if TRUE, cluster rows (or columns) with Hierarchical Clustering ('complete' method).

...
diff --git a/reference/show_sig_bootstrap.html b/reference/show_sig_bootstrap.html index bd710a6d..2e09ec48 100644 --- a/reference/show_sig_bootstrap.html +++ b/reference/show_sig_bootstrap.html @@ -316,29 +316,29 @@

Examples

#> -Summarizing #> -Processing clinical data #> --Missing clinical data -#> -Finished in 0.192s elapsed (0.237s cpu) -#> ℹ [2024-03-08 02:33:54.330123]: Started. -#> ℹ [2024-03-08 02:33:54.334802]: We would assume you marked all variants' position in + strand. -#> ✔ [2024-03-08 02:33:54.33666]: Reference genome loaded. -#> ✔ [2024-03-08 02:33:54.341802]: Variants from MAF object queried. -#> ✔ [2024-03-08 02:33:54.344473]: Chromosome names checked. -#> ✔ [2024-03-08 02:33:54.347903]: Sex chromosomes properly handled. -#> ✔ [2024-03-08 02:33:54.349731]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. -#> ✔ [2024-03-08 02:33:54.356458]: Variant start and end position checked. -#> ✔ [2024-03-08 02:33:54.361336]: Variant data for matrix generation preprocessed. -#> ℹ [2024-03-08 02:33:54.362799]: SBS matrix generation - start. -#> ℹ [2024-03-08 02:33:54.364918]: Extracting 5' and 3' adjacent bases. -#> ℹ [2024-03-08 02:33:54.65857]: Extracting +/- 20bp around mutated bases for background C>T estimation. -#> ℹ [2024-03-08 02:33:55.029449]: Estimating APOBEC enrichment scores. -#> ℹ [2024-03-08 02:33:55.031482]: Performing one-way Fisher's test for APOBEC enrichment. -#> ✔ [2024-03-08 02:33:55.110365]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) -#> ℹ [2024-03-08 02:33:55.113856]: Creating SBS sample-by-component matrices. -#> ✔ [2024-03-08 02:33:55.118188]: SBS-6 matrix created. -#> ✔ [2024-03-08 02:33:55.123134]: SBS-96 matrix created. -#> ✔ [2024-03-08 02:33:55.137189]: SBS-1536 matrix created. -#> ℹ [2024-03-08 02:33:55.139025]: Return SBS-96 as major matrix. -#> ✔ [2024-03-08 02:33:55.141604]: Done. -#> ℹ [2024-03-08 02:33:55.143053]: 0.813 secs elapsed. +#> -Finished in 0.222s elapsed (0.262s cpu) +#> ℹ [2024-03-13 10:48:21.518163]: Started. +#> ℹ [2024-03-13 10:48:21.522936]: We would assume you marked all variants' position in + strand. +#> ✔ [2024-03-13 10:48:21.524829]: Reference genome loaded. +#> ✔ [2024-03-13 10:48:21.52942]: Variants from MAF object queried. +#> ✔ [2024-03-13 10:48:21.531925]: Chromosome names checked. +#> ✔ [2024-03-13 10:48:21.535142]: Sex chromosomes properly handled. +#> ✔ [2024-03-13 10:48:21.536951]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. +#> ✔ [2024-03-13 10:48:21.542449]: Variant start and end position checked. +#> ✔ [2024-03-13 10:48:21.546583]: Variant data for matrix generation preprocessed. +#> ℹ [2024-03-13 10:48:21.548131]: SBS matrix generation - start. +#> ℹ [2024-03-13 10:48:21.550008]: Extracting 5' and 3' adjacent bases. +#> ℹ [2024-03-13 10:48:21.853179]: Extracting +/- 20bp around mutated bases for background C>T estimation. +#> ℹ [2024-03-13 10:48:22.226192]: Estimating APOBEC enrichment scores. +#> ℹ [2024-03-13 10:48:22.228699]: Performing one-way Fisher's test for APOBEC enrichment. +#> ✔ [2024-03-13 10:48:22.311208]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) +#> ℹ [2024-03-13 10:48:22.314861]: Creating SBS sample-by-component matrices. +#> ✔ [2024-03-13 10:48:22.319444]: SBS-6 matrix created. +#> ✔ [2024-03-13 10:48:22.324813]: SBS-96 matrix created. +#> ✔ [2024-03-13 10:48:22.340769]: SBS-1536 matrix created. +#> ℹ [2024-03-13 10:48:22.342319]: Return SBS-96 as major matrix. +#> ✔ [2024-03-13 10:48:22.344906]: Done. +#> ℹ [2024-03-13 10:48:22.346388]: 0.828 secs elapsed. #> The follow samples dropped due to null catalogue: #> TCGA-AB-2823, TCGA-AB-2840, TCGA-AB-2848, TCGA-AB-2909, TCGA-AB-2942 #> NMF algorithm: 'brunet' @@ -347,1119 +347,1119 @@

Examples

#> Runs: | Runs: | | 0% Runs: | Runs: |================= | 33% Runs: | Runs: |================================= | 67% Runs: | Runs: |==================================================| 100% #> System time: #> user system elapsed -#> 6.159 0.000 6.161 -#> ℹ [2024-03-08 02:34:02.752945]: Batch Bootstrap Signature Exposure Analysis Started. -#> ℹ [2024-03-08 02:34:02.754683]: Samples to be filtered out: TCGA-AB-2825,TCGA-AB-2834,TCGA-AB-2866,TCGA-AB-2873,TCGA-AB-2880,TCGA-AB-2883,TCGA-AB-2892,TCGA-AB-2896,TCGA-AB-2903,TCGA-AB-2918,TCGA-AB-2933,TCGA-AB-2948,TCGA-AB-2954 -#> ℹ [2024-03-08 02:34:02.756093]: Finding optimal exposures (&errors) for different methods. -#> ℹ [2024-03-08 02:34:02.757399]: Calling method `QP`. -#> ℹ [2024-03-08 02:34:02.760594]: Started. -#> ℹ [2024-03-08 02:34:02.761888]: Signature index not detected. -#> ✔ [2024-03-08 02:34:02.763218]: Signature object detected. -#> ✔ [2024-03-08 02:34:02.764505]: Database and index checked. -#> ✔ [2024-03-08 02:34:02.765897]: Signature normalized. -#> ℹ [2024-03-08 02:34:02.767204]: Checking row number for catalog matrix and signature matrix. -#> ✔ [2024-03-08 02:34:02.768481]: Checked. -#> ℹ [2024-03-08 02:34:02.769754]: Checking rownames for catalog matrix and signature matrix. -#> ✔ [2024-03-08 02:34:02.771059]: Checked. -#> ✔ [2024-03-08 02:34:02.772342]: Method 'QP' detected. -#> ✔ [2024-03-08 02:34:02.773614]: Corresponding function generated. -#> ℹ [2024-03-08 02:34:02.774898]: Calling function. -#> ℹ [2024-03-08 02:34:02.777014]: Fitting sample: TCGA-AB-2802 -#> ℹ [2024-03-08 02:34:02.778448]: Fitting sample: TCGA-AB-2803 -#> ℹ [2024-03-08 02:34:02.779838]: Fitting sample: TCGA-AB-2804 -#> ℹ [2024-03-08 02:34:02.781188]: Fitting sample: TCGA-AB-2805 -#> ℹ [2024-03-08 02:34:02.782544]: Fitting sample: TCGA-AB-2806 -#> ℹ [2024-03-08 02:34:02.78394]: Fitting sample: TCGA-AB-2807 -#> ℹ [2024-03-08 02:34:02.785286]: Fitting sample: TCGA-AB-2808 -#> ℹ [2024-03-08 02:34:02.786626]: Fitting sample: TCGA-AB-2809 -#> ℹ [2024-03-08 02:34:02.787988]: Fitting sample: TCGA-AB-2810 -#> ℹ [2024-03-08 02:34:02.789335]: Fitting sample: TCGA-AB-2812 -#> ℹ [2024-03-08 02:34:02.790666]: Fitting sample: TCGA-AB-2813 -#> ℹ [2024-03-08 02:34:02.792036]: Fitting sample: TCGA-AB-2814 -#> ℹ [2024-03-08 02:34:02.793368]: Fitting sample: TCGA-AB-2816 -#> ℹ [2024-03-08 02:34:02.794711]: Fitting sample: TCGA-AB-2817 -#> ℹ [2024-03-08 02:34:02.796083]: Fitting sample: TCGA-AB-2818 -#> ℹ [2024-03-08 02:34:02.797434]: Fitting sample: TCGA-AB-2819 -#> ℹ [2024-03-08 02:34:02.798777]: Fitting sample: TCGA-AB-2820 -#> ℹ [2024-03-08 02:34:02.800142]: Fitting sample: TCGA-AB-2821 -#> ℹ [2024-03-08 02:34:02.801487]: Fitting sample: TCGA-AB-2822 -#> ℹ [2024-03-08 02:34:02.802857]: Fitting sample: TCGA-AB-2824 -#> ℹ [2024-03-08 02:34:02.804203]: Fitting sample: TCGA-AB-2826 -#> ℹ [2024-03-08 02:34:02.80554]: Fitting sample: TCGA-AB-2827 -#> ℹ [2024-03-08 02:34:02.806901]: Fitting sample: TCGA-AB-2828 -#> ℹ [2024-03-08 02:34:02.808254]: Fitting sample: TCGA-AB-2829 -#> ℹ [2024-03-08 02:34:02.809599]: Fitting sample: TCGA-AB-2830 -#> ℹ [2024-03-08 02:34:02.810984]: Fitting sample: TCGA-AB-2831 -#> ℹ [2024-03-08 02:34:02.81235]: Fitting sample: TCGA-AB-2832 -#> ℹ [2024-03-08 02:34:02.813697]: Fitting sample: TCGA-AB-2833 -#> ℹ [2024-03-08 02:34:02.815064]: Fitting sample: TCGA-AB-2835 -#> ℹ [2024-03-08 02:34:02.816426]: Fitting sample: TCGA-AB-2836 -#> ℹ [2024-03-08 02:34:02.817779]: Fitting sample: TCGA-AB-2838 -#> ℹ [2024-03-08 02:34:02.819168]: Fitting sample: TCGA-AB-2839 -#> ℹ [2024-03-08 02:34:02.820514]: Fitting sample: TCGA-AB-2841 -#> ℹ [2024-03-08 02:34:02.821896]: Fitting sample: TCGA-AB-2842 -#> ℹ [2024-03-08 02:34:02.823266]: Fitting sample: TCGA-AB-2843 -#> ℹ [2024-03-08 02:34:02.824614]: Fitting sample: TCGA-AB-2844 -#> ℹ [2024-03-08 02:34:02.82596]: Fitting sample: TCGA-AB-2845 -#> ℹ [2024-03-08 02:34:02.827334]: Fitting sample: TCGA-AB-2846 -#> ℹ [2024-03-08 02:34:02.828679]: Fitting sample: TCGA-AB-2847 -#> ℹ [2024-03-08 02:34:02.830027]: Fitting sample: TCGA-AB-2849 -#> ℹ [2024-03-08 02:34:02.831397]: Fitting sample: TCGA-AB-2850 -#> ℹ [2024-03-08 02:34:02.83276]: Fitting sample: TCGA-AB-2851 -#> ℹ [2024-03-08 02:34:02.83411]: Fitting sample: TCGA-AB-2853 -#> ℹ [2024-03-08 02:34:02.835492]: Fitting sample: TCGA-AB-2854 -#> ℹ [2024-03-08 02:34:02.836842]: Fitting sample: TCGA-AB-2855 -#> ℹ [2024-03-08 02:34:02.838193]: Fitting sample: TCGA-AB-2857 -#> ℹ [2024-03-08 02:34:02.839573]: Fitting sample: TCGA-AB-2858 -#> ℹ [2024-03-08 02:34:02.840935]: Fitting sample: TCGA-AB-2859 -#> ℹ [2024-03-08 02:34:02.842276]: Fitting sample: TCGA-AB-2860 -#> ℹ [2024-03-08 02:34:02.843658]: Fitting sample: TCGA-AB-2861 -#> ℹ [2024-03-08 02:34:02.845002]: Fitting sample: TCGA-AB-2862 -#> ℹ [2024-03-08 02:34:02.846346]: Fitting sample: TCGA-AB-2863 -#> ℹ [2024-03-08 02:34:02.847713]: Fitting sample: TCGA-AB-2864 -#> ℹ [2024-03-08 02:34:02.849058]: Fitting sample: TCGA-AB-2865 -#> ℹ [2024-03-08 02:34:02.850404]: Fitting sample: TCGA-AB-2867 -#> ℹ [2024-03-08 02:34:02.851781]: Fitting sample: TCGA-AB-2868 -#> ℹ [2024-03-08 02:34:02.853212]: Fitting sample: TCGA-AB-2869 -#> ℹ [2024-03-08 02:34:02.854568]: Fitting sample: TCGA-AB-2870 -#> ℹ [2024-03-08 02:34:02.855947]: Fitting sample: TCGA-AB-2871 -#> ℹ [2024-03-08 02:34:02.857312]: Fitting sample: TCGA-AB-2872 -#> ℹ [2024-03-08 02:34:02.858667]: Fitting sample: TCGA-AB-2874 -#> ℹ [2024-03-08 02:34:02.860043]: Fitting sample: TCGA-AB-2875 -#> ℹ [2024-03-08 02:34:02.86139]: Fitting sample: TCGA-AB-2876 -#> ℹ [2024-03-08 02:34:02.862749]: Fitting sample: TCGA-AB-2877 -#> ℹ [2024-03-08 02:34:02.864107]: Fitting sample: TCGA-AB-2878 -#> ℹ [2024-03-08 02:34:02.865447]: Fitting sample: TCGA-AB-2879 -#> ℹ [2024-03-08 02:34:02.866793]: Fitting sample: TCGA-AB-2881 -#> ℹ [2024-03-08 02:34:02.86815]: Fitting sample: TCGA-AB-2882 -#> ℹ [2024-03-08 02:34:02.869594]: Fitting sample: TCGA-AB-2884 -#> ℹ [2024-03-08 02:34:02.870973]: Fitting sample: TCGA-AB-2885 -#> ℹ [2024-03-08 02:34:02.872336]: Fitting sample: TCGA-AB-2886 -#> ℹ [2024-03-08 02:34:02.873696]: Fitting sample: TCGA-AB-2887 -#> ℹ [2024-03-08 02:34:02.875063]: Fitting sample: TCGA-AB-2888 -#> ℹ [2024-03-08 02:34:02.87642]: Fitting sample: TCGA-AB-2889 -#> ℹ [2024-03-08 02:34:02.877779]: Fitting sample: TCGA-AB-2890 -#> ℹ [2024-03-08 02:34:02.879147]: Fitting sample: TCGA-AB-2891 -#> ℹ [2024-03-08 02:34:02.880494]: Fitting sample: TCGA-AB-2894 -#> ℹ [2024-03-08 02:34:02.881848]: Fitting sample: TCGA-AB-2895 -#> ℹ [2024-03-08 02:34:02.883206]: Fitting sample: TCGA-AB-2897 -#> ℹ [2024-03-08 02:34:02.884553]: Fitting sample: TCGA-AB-2898 -#> ℹ [2024-03-08 02:34:02.885904]: Fitting sample: TCGA-AB-2899 -#> ℹ [2024-03-08 02:34:02.88729]: Fitting sample: TCGA-AB-2900 -#> ℹ [2024-03-08 02:34:02.888649]: Fitting sample: TCGA-AB-2901 -#> ℹ [2024-03-08 02:34:02.890006]: Fitting sample: TCGA-AB-2904 -#> ℹ [2024-03-08 02:34:02.891388]: Fitting sample: TCGA-AB-2905 -#> ℹ [2024-03-08 02:34:02.892749]: Fitting sample: TCGA-AB-2906 -#> ℹ [2024-03-08 02:34:02.894094]: Fitting sample: TCGA-AB-2907 -#> ℹ [2024-03-08 02:34:02.895463]: Fitting sample: TCGA-AB-2908 -#> ℹ [2024-03-08 02:34:02.896812]: Fitting sample: TCGA-AB-2910 -#> ℹ [2024-03-08 02:34:02.898161]: Fitting sample: TCGA-AB-2911 -#> ℹ [2024-03-08 02:34:02.899532]: Fitting sample: TCGA-AB-2912 -#> ℹ [2024-03-08 02:34:02.900879]: Fitting sample: TCGA-AB-2913 -#> ℹ [2024-03-08 02:34:02.902229]: Fitting sample: TCGA-AB-2914 -#> ℹ [2024-03-08 02:34:02.903635]: Fitting sample: TCGA-AB-2915 -#> ℹ [2024-03-08 02:34:02.905]: Fitting sample: TCGA-AB-2916 -#> ℹ [2024-03-08 02:34:02.906362]: Fitting sample: TCGA-AB-2917 -#> ℹ [2024-03-08 02:34:02.90774]: Fitting sample: TCGA-AB-2919 -#> ℹ [2024-03-08 02:34:02.909083]: Fitting sample: TCGA-AB-2920 -#> ℹ [2024-03-08 02:34:02.91045]: Fitting sample: TCGA-AB-2921 -#> ℹ [2024-03-08 02:34:02.911836]: Fitting sample: TCGA-AB-2922 -#> ℹ [2024-03-08 02:34:02.913194]: Fitting sample: TCGA-AB-2923 -#> ℹ [2024-03-08 02:34:02.914544]: Fitting sample: TCGA-AB-2924 -#> ℹ [2024-03-08 02:34:02.915968]: Fitting sample: TCGA-AB-2925 -#> ℹ [2024-03-08 02:34:02.917648]: Fitting sample: TCGA-AB-2926 -#> ℹ [2024-03-08 02:34:02.919791]: Fitting sample: TCGA-AB-2927 -#> ℹ [2024-03-08 02:34:02.9218]: Fitting sample: TCGA-AB-2928 -#> ℹ [2024-03-08 02:34:02.923808]: Fitting sample: TCGA-AB-2929 -#> ℹ [2024-03-08 02:34:02.925818]: Fitting sample: TCGA-AB-2930 -#> ℹ [2024-03-08 02:34:02.927872]: Fitting sample: TCGA-AB-2931 -#> ℹ [2024-03-08 02:34:02.929875]: Fitting sample: TCGA-AB-2932 -#> ℹ [2024-03-08 02:34:02.931885]: Fitting sample: TCGA-AB-2934 -#> ℹ [2024-03-08 02:34:02.933856]: Fitting sample: TCGA-AB-2935 -#> ℹ [2024-03-08 02:34:02.935713]: Fitting sample: TCGA-AB-2936 -#> ℹ [2024-03-08 02:34:02.937087]: Fitting sample: TCGA-AB-2937 -#> ℹ [2024-03-08 02:34:02.938442]: Fitting sample: TCGA-AB-2938 -#> ℹ [2024-03-08 02:34:02.939838]: Fitting sample: TCGA-AB-2939 -#> ℹ [2024-03-08 02:34:02.941183]: Fitting sample: TCGA-AB-2940 -#> ℹ [2024-03-08 02:34:02.942534]: Fitting sample: TCGA-AB-2941 -#> ℹ [2024-03-08 02:34:02.943921]: Fitting sample: TCGA-AB-2943 -#> ℹ [2024-03-08 02:34:02.945265]: Fitting sample: TCGA-AB-2945 -#> ℹ [2024-03-08 02:34:02.946614]: Fitting sample: TCGA-AB-2946 -#> ℹ [2024-03-08 02:34:02.948038]: Fitting sample: TCGA-AB-2947 -#> ℹ [2024-03-08 02:34:02.949394]: Fitting sample: TCGA-AB-2949 -#> ℹ [2024-03-08 02:34:02.950738]: Fitting sample: TCGA-AB-2950 -#> ℹ [2024-03-08 02:34:02.952144]: Fitting sample: TCGA-AB-2952 -#> ℹ [2024-03-08 02:34:02.953486]: Fitting sample: TCGA-AB-2955 -#> ℹ [2024-03-08 02:34:02.954859]: Fitting sample: TCGA-AB-2956 -#> ℹ [2024-03-08 02:34:02.956209]: Fitting sample: TCGA-AB-2957 -#> ℹ [2024-03-08 02:34:02.957554]: Fitting sample: TCGA-AB-2959 -#> ℹ [2024-03-08 02:34:02.95892]: Fitting sample: TCGA-AB-2963 -#> ℹ [2024-03-08 02:34:02.960266]: Fitting sample: TCGA-AB-2964 -#> ℹ [2024-03-08 02:34:02.961617]: Fitting sample: TCGA-AB-2965 -#> ℹ [2024-03-08 02:34:02.962985]: Fitting sample: TCGA-AB-2966 -#> ℹ [2024-03-08 02:34:02.964331]: Fitting sample: TCGA-AB-2967 -#> ℹ [2024-03-08 02:34:02.965683]: Fitting sample: TCGA-AB-2968 -#> ℹ [2024-03-08 02:34:02.967059]: Fitting sample: TCGA-AB-2970 -#> ℹ [2024-03-08 02:34:02.968408]: Fitting sample: TCGA-AB-2971 -#> ℹ [2024-03-08 02:34:02.969768]: Fitting sample: TCGA-AB-2972 -#> ℹ [2024-03-08 02:34:02.971134]: Fitting sample: TCGA-AB-2973 -#> ℹ [2024-03-08 02:34:02.972492]: Fitting sample: TCGA-AB-2974 -#> ℹ [2024-03-08 02:34:02.973836]: Fitting sample: TCGA-AB-2975 -#> ℹ [2024-03-08 02:34:02.975204]: Fitting sample: TCGA-AB-2976 -#> ℹ [2024-03-08 02:34:02.976554]: Fitting sample: TCGA-AB-2977 -#> ℹ [2024-03-08 02:34:02.977901]: Fitting sample: TCGA-AB-2978 -#> ℹ [2024-03-08 02:34:02.979272]: Fitting sample: TCGA-AB-2979 -#> ℹ [2024-03-08 02:34:02.98062]: Fitting sample: TCGA-AB-2980 -#> ℹ [2024-03-08 02:34:02.981988]: Fitting sample: TCGA-AB-2981 -#> ℹ [2024-03-08 02:34:02.983361]: Fitting sample: TCGA-AB-2982 -#> ℹ [2024-03-08 02:34:02.98472]: Fitting sample: TCGA-AB-2983 -#> ℹ [2024-03-08 02:34:02.986061]: Fitting sample: TCGA-AB-2984 -#> ℹ [2024-03-08 02:34:02.987455]: Fitting sample: TCGA-AB-2985 -#> ℹ [2024-03-08 02:34:02.988819]: Fitting sample: TCGA-AB-2986 -#> ℹ [2024-03-08 02:34:02.990169]: Fitting sample: TCGA-AB-2987 -#> ℹ [2024-03-08 02:34:02.991534]: Fitting sample: TCGA-AB-2988 -#> ℹ [2024-03-08 02:34:02.992883]: Fitting sample: TCGA-AB-2989 -#> ℹ [2024-03-08 02:34:02.994223]: Fitting sample: TCGA-AB-2990 -#> ℹ [2024-03-08 02:34:02.995589]: Fitting sample: TCGA-AB-2991 -#> ℹ [2024-03-08 02:34:02.996941]: Fitting sample: TCGA-AB-2992 -#> ℹ [2024-03-08 02:34:02.99828]: Fitting sample: TCGA-AB-2993 -#> ℹ [2024-03-08 02:34:02.999656]: Fitting sample: TCGA-AB-2994 -#> ℹ [2024-03-08 02:34:03.000999]: Fitting sample: TCGA-AB-2995 -#> ℹ [2024-03-08 02:34:03.002364]: Fitting sample: TCGA-AB-2996 -#> ℹ [2024-03-08 02:34:03.003752]: Fitting sample: TCGA-AB-2997 -#> ℹ [2024-03-08 02:34:03.005108]: Fitting sample: TCGA-AB-2998 -#> ℹ [2024-03-08 02:34:03.006459]: Fitting sample: TCGA-AB-2999 -#> ℹ [2024-03-08 02:34:03.007833]: Fitting sample: TCGA-AB-3000 -#> ℹ [2024-03-08 02:34:03.009178]: Fitting sample: TCGA-AB-3001 -#> ℹ [2024-03-08 02:34:03.010529]: Fitting sample: TCGA-AB-3002 -#> ℹ [2024-03-08 02:34:03.011908]: Fitting sample: TCGA-AB-3005 -#> ℹ [2024-03-08 02:34:03.013259]: Fitting sample: TCGA-AB-3006 -#> ℹ [2024-03-08 02:34:03.01461]: Fitting sample: TCGA-AB-3007 -#> ℹ [2024-03-08 02:34:03.015985]: Fitting sample: TCGA-AB-3008 -#> ℹ [2024-03-08 02:34:03.017434]: Fitting sample: TCGA-AB-3009 -#> ℹ [2024-03-08 02:34:03.018781]: Fitting sample: TCGA-AB-3011 -#> ℹ [2024-03-08 02:34:03.020149]: Fitting sample: TCGA-AB-3012 -#> ✔ [2024-03-08 02:34:03.0215]: Done. -#> ℹ [2024-03-08 02:34:03.022867]: Generating output signature exposures. -#> ✔ [2024-03-08 02:34:03.03697]: Done. -#> ℹ [2024-03-08 02:34:03.038361]: Calculating errors (Frobenius Norm). -#> ✔ [2024-03-08 02:34:03.071875]: Done. -#> ℹ [2024-03-08 02:34:03.074081]: 0.313 secs elapsed. -#> ℹ [2024-03-08 02:34:03.077287]: Getting bootstrap exposures (&errors/similarity) for different methods. -#> ℹ [2024-03-08 02:34:03.078628]: This step is time consuming, please be patient. -#> ℹ [2024-03-08 02:34:03.080567]: Processing sample `TCGA-AB-2802`. -#> ℹ [2024-03-08 02:34:04.130048]: Processing sample `TCGA-AB-2803`. -#> ℹ [2024-03-08 02:34:05.186416]: Processing sample `TCGA-AB-2804`. -#> ℹ [2024-03-08 02:34:06.225231]: Processing sample `TCGA-AB-2805`. -#> ℹ [2024-03-08 02:34:07.279073]: Processing sample `TCGA-AB-2806`. -#> ℹ [2024-03-08 02:34:08.320622]: Processing sample `TCGA-AB-2807`. -#> ℹ [2024-03-08 02:34:09.355083]: Processing sample `TCGA-AB-2808`. -#> ℹ [2024-03-08 02:34:10.398388]: Processing sample `TCGA-AB-2809`. -#> ℹ [2024-03-08 02:34:11.452439]: Processing sample `TCGA-AB-2810`. -#> ℹ [2024-03-08 02:34:12.493036]: Processing sample `TCGA-AB-2812`. -#> ℹ [2024-03-08 02:34:13.533991]: Processing sample `TCGA-AB-2813`. -#> ℹ [2024-03-08 02:34:14.574434]: Processing sample `TCGA-AB-2814`. -#> ℹ [2024-03-08 02:34:15.617062]: Processing sample `TCGA-AB-2816`. -#> ℹ [2024-03-08 02:34:16.664858]: Processing sample `TCGA-AB-2817`. -#> ℹ [2024-03-08 02:34:17.69767]: Processing sample `TCGA-AB-2818`. -#> ℹ [2024-03-08 02:34:18.737506]: Processing sample `TCGA-AB-2819`. -#> ℹ [2024-03-08 02:34:19.783906]: Processing sample `TCGA-AB-2820`. -#> ℹ [2024-03-08 02:34:20.835348]: Processing sample `TCGA-AB-2821`. -#> ℹ [2024-03-08 02:34:21.873014]: Processing sample `TCGA-AB-2822`. -#> ℹ [2024-03-08 02:34:22.918753]: Processing sample `TCGA-AB-2824`. -#> ℹ [2024-03-08 02:34:23.975012]: Processing sample `TCGA-AB-2826`. -#> ℹ [2024-03-08 02:34:25.009706]: Processing sample `TCGA-AB-2827`. -#> ℹ [2024-03-08 02:34:26.049602]: Processing sample `TCGA-AB-2828`. -#> ℹ [2024-03-08 02:34:27.093591]: Processing sample `TCGA-AB-2829`. -#> ℹ [2024-03-08 02:34:28.147758]: Processing sample `TCGA-AB-2830`. -#> ℹ [2024-03-08 02:34:29.180896]: Processing sample `TCGA-AB-2831`. -#> ℹ [2024-03-08 02:34:30.231118]: Processing sample `TCGA-AB-2832`. -#> ℹ [2024-03-08 02:34:31.283348]: Processing sample `TCGA-AB-2833`. -#> ℹ [2024-03-08 02:34:32.328062]: Processing sample `TCGA-AB-2835`. -#> ℹ [2024-03-08 02:34:33.374195]: Processing sample `TCGA-AB-2836`. -#> ℹ [2024-03-08 02:34:34.415743]: Processing sample `TCGA-AB-2838`. -#> ℹ [2024-03-08 02:34:35.446631]: Processing sample `TCGA-AB-2839`. -#> ℹ [2024-03-08 02:34:36.484753]: Processing sample `TCGA-AB-2841`. -#> ℹ [2024-03-08 02:34:37.535314]: Processing sample `TCGA-AB-2842`. -#> ℹ [2024-03-08 02:34:38.576813]: Processing sample `TCGA-AB-2843`. -#> ℹ [2024-03-08 02:34:39.625127]: Processing sample `TCGA-AB-2844`. -#> ℹ [2024-03-08 02:34:40.67606]: Processing sample `TCGA-AB-2845`. -#> ℹ [2024-03-08 02:34:41.73212]: Processing sample `TCGA-AB-2846`. -#> ℹ [2024-03-08 02:34:42.776196]: Processing sample `TCGA-AB-2847`. -#> ℹ [2024-03-08 02:34:43.827737]: Processing sample `TCGA-AB-2849`. -#> ℹ [2024-03-08 02:34:44.881774]: Processing sample `TCGA-AB-2850`. -#> ℹ [2024-03-08 02:34:45.929462]: Processing sample `TCGA-AB-2851`. -#> ℹ [2024-03-08 02:34:46.97939]: Processing sample `TCGA-AB-2853`. -#> ℹ [2024-03-08 02:34:48.025217]: Processing sample `TCGA-AB-2854`. -#> ℹ [2024-03-08 02:34:49.067221]: Processing sample `TCGA-AB-2855`. -#> ℹ [2024-03-08 02:34:50.11711]: Processing sample `TCGA-AB-2857`. -#> ℹ [2024-03-08 02:34:51.171926]: Processing sample `TCGA-AB-2858`. -#> ℹ [2024-03-08 02:34:52.22524]: Processing sample `TCGA-AB-2859`. -#> ℹ [2024-03-08 02:34:53.273555]: Processing sample `TCGA-AB-2860`. -#> ℹ [2024-03-08 02:34:54.32337]: Processing sample `TCGA-AB-2861`. -#> ℹ [2024-03-08 02:34:55.372787]: Processing sample `TCGA-AB-2862`. -#> ℹ [2024-03-08 02:34:56.424027]: Processing sample `TCGA-AB-2863`. -#> ℹ [2024-03-08 02:34:57.466764]: Processing sample `TCGA-AB-2864`. -#> ℹ [2024-03-08 02:34:58.513383]: Processing sample `TCGA-AB-2865`. -#> ℹ [2024-03-08 02:34:59.572774]: Processing sample `TCGA-AB-2867`. -#> ℹ [2024-03-08 02:35:00.62938]: Processing sample `TCGA-AB-2868`. -#> ℹ [2024-03-08 02:35:01.686942]: Processing sample `TCGA-AB-2869`. -#> ℹ [2024-03-08 02:35:02.755234]: Processing sample `TCGA-AB-2870`. -#> ℹ [2024-03-08 02:35:03.805262]: Processing sample `TCGA-AB-2871`. -#> ℹ [2024-03-08 02:35:04.854396]: Processing sample `TCGA-AB-2872`. -#> ℹ [2024-03-08 02:35:05.908565]: Processing sample `TCGA-AB-2874`. -#> ℹ [2024-03-08 02:35:06.951283]: Processing sample `TCGA-AB-2875`. -#> ℹ [2024-03-08 02:35:08.002697]: Processing sample `TCGA-AB-2876`. -#> ℹ [2024-03-08 02:35:09.05936]: Processing sample `TCGA-AB-2877`. -#> ℹ [2024-03-08 02:35:10.114435]: Processing sample `TCGA-AB-2878`. -#> ℹ [2024-03-08 02:35:11.16256]: Processing sample `TCGA-AB-2879`. -#> ℹ [2024-03-08 02:35:12.213039]: Processing sample `TCGA-AB-2881`. -#> ℹ [2024-03-08 02:35:13.258426]: Processing sample `TCGA-AB-2882`. -#> ℹ [2024-03-08 02:35:14.300577]: Processing sample `TCGA-AB-2884`. -#> ℹ [2024-03-08 02:35:15.348886]: Processing sample `TCGA-AB-2885`. -#> ℹ [2024-03-08 02:35:16.396717]: Processing sample `TCGA-AB-2886`. -#> ℹ [2024-03-08 02:35:17.445777]: Processing sample `TCGA-AB-2887`. -#> ℹ [2024-03-08 02:35:18.504936]: Processing sample `TCGA-AB-2888`. -#> ℹ [2024-03-08 02:35:19.545557]: Processing sample `TCGA-AB-2889`. -#> ℹ [2024-03-08 02:35:20.58961]: Processing sample `TCGA-AB-2890`. -#> ℹ [2024-03-08 02:35:21.637243]: Processing sample `TCGA-AB-2891`. -#> ℹ [2024-03-08 02:35:22.685937]: Processing sample `TCGA-AB-2894`. -#> ℹ [2024-03-08 02:35:23.741261]: Processing sample `TCGA-AB-2895`. -#> ℹ [2024-03-08 02:35:24.790902]: Processing sample `TCGA-AB-2897`. -#> ℹ [2024-03-08 02:35:25.842478]: Processing sample `TCGA-AB-2898`. -#> ℹ [2024-03-08 02:35:26.893712]: Processing sample `TCGA-AB-2899`. -#> ℹ [2024-03-08 02:35:27.940643]: Processing sample `TCGA-AB-2900`. -#> ℹ [2024-03-08 02:35:28.982556]: Processing sample `TCGA-AB-2901`. -#> ℹ [2024-03-08 02:35:30.022598]: Processing sample `TCGA-AB-2904`. -#> ℹ [2024-03-08 02:35:31.064806]: Processing sample `TCGA-AB-2905`. -#> ℹ [2024-03-08 02:35:32.092963]: Processing sample `TCGA-AB-2906`. -#> ℹ [2024-03-08 02:35:33.133644]: Processing sample `TCGA-AB-2907`. -#> ℹ [2024-03-08 02:35:34.167599]: Processing sample `TCGA-AB-2908`. -#> ℹ [2024-03-08 02:35:35.206758]: Processing sample `TCGA-AB-2910`. -#> ℹ [2024-03-08 02:35:36.255249]: Processing sample `TCGA-AB-2911`. -#> ℹ [2024-03-08 02:35:37.283375]: Processing sample `TCGA-AB-2912`. -#> ℹ [2024-03-08 02:35:38.31589]: Processing sample `TCGA-AB-2913`. -#> ℹ [2024-03-08 02:35:39.347018]: Processing sample `TCGA-AB-2914`. -#> ℹ [2024-03-08 02:35:40.375337]: Processing sample `TCGA-AB-2915`. -#> ℹ [2024-03-08 02:35:41.398194]: Processing sample `TCGA-AB-2916`. -#> ℹ [2024-03-08 02:35:42.423164]: Processing sample `TCGA-AB-2917`. -#> ℹ [2024-03-08 02:35:43.454373]: Processing sample `TCGA-AB-2919`. -#> ℹ [2024-03-08 02:35:44.482941]: Processing sample `TCGA-AB-2920`. -#> ℹ [2024-03-08 02:35:45.506288]: Processing sample `TCGA-AB-2921`. -#> ℹ [2024-03-08 02:35:46.52658]: Processing sample `TCGA-AB-2922`. -#> ℹ [2024-03-08 02:35:47.55585]: Processing sample `TCGA-AB-2923`. -#> ℹ [2024-03-08 02:35:48.584943]: Processing sample `TCGA-AB-2924`. -#> ℹ [2024-03-08 02:35:49.619668]: Processing sample `TCGA-AB-2925`. -#> ℹ [2024-03-08 02:35:50.644983]: Processing sample `TCGA-AB-2926`. -#> ℹ [2024-03-08 02:35:51.666836]: Processing sample `TCGA-AB-2927`. -#> ℹ [2024-03-08 02:35:52.69042]: Processing sample `TCGA-AB-2928`. -#> ℹ [2024-03-08 02:35:53.713766]: Processing sample `TCGA-AB-2929`. -#> ℹ [2024-03-08 02:35:54.749472]: Processing sample `TCGA-AB-2930`. -#> ℹ [2024-03-08 02:35:55.772796]: Processing sample `TCGA-AB-2931`. -#> ℹ [2024-03-08 02:35:56.78837]: Processing sample `TCGA-AB-2932`. -#> ℹ [2024-03-08 02:35:57.833552]: Processing sample `TCGA-AB-2934`. -#> ℹ [2024-03-08 02:35:58.883661]: Processing sample `TCGA-AB-2935`. -#> ℹ [2024-03-08 02:35:59.884506]: Processing sample `TCGA-AB-2936`. -#> ℹ [2024-03-08 02:36:00.887614]: Processing sample `TCGA-AB-2937`. -#> ℹ [2024-03-08 02:36:01.888325]: Processing sample `TCGA-AB-2938`. -#> ℹ [2024-03-08 02:36:02.893572]: Processing sample `TCGA-AB-2939`. -#> ℹ [2024-03-08 02:36:03.891221]: Processing sample `TCGA-AB-2940`. -#> ℹ [2024-03-08 02:36:04.887788]: Processing sample `TCGA-AB-2941`. -#> ℹ [2024-03-08 02:36:05.891335]: Processing sample `TCGA-AB-2943`. -#> ℹ [2024-03-08 02:36:06.903765]: Processing sample `TCGA-AB-2945`. -#> ℹ [2024-03-08 02:36:07.909167]: Processing sample `TCGA-AB-2946`. -#> ℹ [2024-03-08 02:36:08.922143]: Processing sample `TCGA-AB-2947`. -#> ℹ [2024-03-08 02:36:09.929782]: Processing sample `TCGA-AB-2949`. -#> ℹ [2024-03-08 02:36:10.948011]: Processing sample `TCGA-AB-2950`. -#> ℹ [2024-03-08 02:36:11.969723]: Processing sample `TCGA-AB-2952`. -#> ℹ [2024-03-08 02:36:12.983778]: Processing sample `TCGA-AB-2955`. -#> ℹ [2024-03-08 02:36:14.007283]: Processing sample `TCGA-AB-2956`. -#> ℹ [2024-03-08 02:36:15.026148]: Processing sample `TCGA-AB-2957`. -#> ℹ [2024-03-08 02:36:16.045235]: Processing sample `TCGA-AB-2959`. -#> ℹ [2024-03-08 02:36:17.09935]: Processing sample `TCGA-AB-2963`. -#> ℹ [2024-03-08 02:36:18.149919]: Processing sample `TCGA-AB-2964`. -#> ℹ [2024-03-08 02:36:19.177149]: Processing sample `TCGA-AB-2965`. -#> ℹ [2024-03-08 02:36:20.205383]: Processing sample `TCGA-AB-2966`. -#> ℹ [2024-03-08 02:36:21.211502]: Processing sample `TCGA-AB-2967`. -#> ℹ [2024-03-08 02:36:22.208664]: Processing sample `TCGA-AB-2968`. -#> ℹ [2024-03-08 02:36:23.216861]: Processing sample `TCGA-AB-2970`. -#> ℹ [2024-03-08 02:36:24.241102]: Processing sample `TCGA-AB-2971`. -#> ℹ [2024-03-08 02:36:25.248761]: Processing sample `TCGA-AB-2972`. -#> ℹ [2024-03-08 02:36:26.2465]: Processing sample `TCGA-AB-2973`. -#> ℹ [2024-03-08 02:36:27.255313]: Processing sample `TCGA-AB-2974`. -#> ℹ [2024-03-08 02:36:28.277634]: Processing sample `TCGA-AB-2975`. -#> ℹ [2024-03-08 02:36:29.279826]: Processing sample `TCGA-AB-2976`. -#> ℹ [2024-03-08 02:36:30.298744]: Processing sample `TCGA-AB-2977`. -#> ℹ [2024-03-08 02:36:31.311939]: Processing sample `TCGA-AB-2978`. -#> ℹ [2024-03-08 02:36:32.327556]: Processing sample `TCGA-AB-2979`. -#> ℹ [2024-03-08 02:36:33.346462]: Processing sample `TCGA-AB-2980`. -#> ℹ [2024-03-08 02:36:34.351095]: Processing sample `TCGA-AB-2981`. -#> ℹ [2024-03-08 02:36:35.348991]: Processing sample `TCGA-AB-2982`. -#> ℹ [2024-03-08 02:36:36.344976]: Processing sample `TCGA-AB-2983`. -#> ℹ [2024-03-08 02:36:37.346141]: Processing sample `TCGA-AB-2984`. -#> ℹ [2024-03-08 02:36:38.340612]: Processing sample `TCGA-AB-2985`. -#> ℹ [2024-03-08 02:36:39.333265]: Processing sample `TCGA-AB-2986`. -#> ℹ [2024-03-08 02:36:40.33369]: Processing sample `TCGA-AB-2987`. -#> ℹ [2024-03-08 02:36:41.331659]: Processing sample `TCGA-AB-2988`. -#> ℹ [2024-03-08 02:36:42.3258]: Processing sample `TCGA-AB-2989`. -#> ℹ [2024-03-08 02:36:43.326462]: Processing sample `TCGA-AB-2990`. -#> ℹ [2024-03-08 02:36:44.321866]: Processing sample `TCGA-AB-2991`. -#> ℹ [2024-03-08 02:36:45.319446]: Processing sample `TCGA-AB-2992`. -#> ℹ [2024-03-08 02:36:46.315019]: Processing sample `TCGA-AB-2993`. -#> ℹ [2024-03-08 02:36:47.307639]: Processing sample `TCGA-AB-2994`. -#> ℹ [2024-03-08 02:36:48.304245]: Processing sample `TCGA-AB-2995`. -#> ℹ [2024-03-08 02:36:49.293662]: Processing sample `TCGA-AB-2996`. -#> ℹ [2024-03-08 02:36:50.288381]: Processing sample `TCGA-AB-2997`. -#> ℹ [2024-03-08 02:36:51.27933]: Processing sample `TCGA-AB-2998`. -#> ℹ [2024-03-08 02:36:52.271555]: Processing sample `TCGA-AB-2999`. -#> ℹ [2024-03-08 02:36:53.264516]: Processing sample `TCGA-AB-3000`. -#> ℹ [2024-03-08 02:36:54.258618]: Processing sample `TCGA-AB-3001`. -#> ℹ [2024-03-08 02:36:55.25262]: Processing sample `TCGA-AB-3002`. -#> ℹ [2024-03-08 02:36:56.248875]: Processing sample `TCGA-AB-3005`. -#> ℹ [2024-03-08 02:36:57.241746]: Processing sample `TCGA-AB-3006`. -#> ℹ [2024-03-08 02:36:58.237482]: Processing sample `TCGA-AB-3007`. -#> ℹ [2024-03-08 02:36:59.230435]: Processing sample `TCGA-AB-3008`. -#> ℹ [2024-03-08 02:37:00.244108]: Processing sample `TCGA-AB-3009`. -#> ℹ [2024-03-08 02:37:01.23717]: Processing sample `TCGA-AB-3011`. -#> ℹ [2024-03-08 02:37:02.228112]: Processing sample `TCGA-AB-3012`. -#> ✔ [2024-03-08 02:37:03.224198]: Gotten. -#> ℹ [2024-03-08 02:37:03.226618]: Reporting p values... -#> ℹ [2024-03-08 02:37:03.228435]: Started. -#> ✔ [2024-03-08 02:37:03.229933]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.23203]: Done. -#> ℹ [2024-03-08 02:37:03.233476]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.234928]: Started. -#> ✔ [2024-03-08 02:37:03.236269]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.238027]: Done. -#> ℹ [2024-03-08 02:37:03.239418]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.240774]: Started. -#> ✔ [2024-03-08 02:37:03.242069]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.243832]: Done. -#> ℹ [2024-03-08 02:37:03.245178]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.24652]: Started. -#> ✔ [2024-03-08 02:37:03.247836]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.249539]: Done. -#> ℹ [2024-03-08 02:37:03.250914]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.252264]: Started. -#> ✔ [2024-03-08 02:37:03.253547]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.255245]: Done. -#> ℹ [2024-03-08 02:37:03.25658]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.257912]: Started. -#> ✔ [2024-03-08 02:37:03.259233]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.260923]: Done. -#> ℹ [2024-03-08 02:37:03.262257]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.26361]: Started. -#> ✔ [2024-03-08 02:37:03.264895]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.266583]: Done. -#> ℹ [2024-03-08 02:37:03.267941]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.269257]: Started. -#> ✔ [2024-03-08 02:37:03.270535]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.272249]: Done. -#> ℹ [2024-03-08 02:37:03.273598]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.27494]: Started. -#> ✔ [2024-03-08 02:37:03.276226]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.2779]: Done. -#> ℹ [2024-03-08 02:37:03.279252]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.280569]: Started. -#> ✔ [2024-03-08 02:37:03.281849]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.283572]: Done. -#> ℹ [2024-03-08 02:37:03.284901]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.286218]: Started. -#> ✔ [2024-03-08 02:37:03.287515]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.289185]: Done. -#> ℹ [2024-03-08 02:37:03.290512]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.291858]: Started. -#> ✔ [2024-03-08 02:37:03.29314]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.294849]: Done. -#> ℹ [2024-03-08 02:37:03.296186]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.29751]: Started. -#> ✔ [2024-03-08 02:37:03.298777]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.300472]: Done. -#> ℹ [2024-03-08 02:37:03.301798]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.303151]: Started. -#> ✔ [2024-03-08 02:37:03.304452]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.30616]: Done. -#> ℹ [2024-03-08 02:37:03.307532]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.30886]: Started. -#> ✔ [2024-03-08 02:37:03.310142]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.311845]: Done. -#> ℹ [2024-03-08 02:37:03.313188]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.314506]: Started. -#> ✔ [2024-03-08 02:37:03.315809]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.317486]: Done. -#> ℹ [2024-03-08 02:37:03.318809]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.320145]: Started. -#> ✔ [2024-03-08 02:37:03.32142]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.32312]: Done. -#> ℹ [2024-03-08 02:37:03.324448]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.32576]: Started. -#> ✔ [2024-03-08 02:37:03.327058]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.328746]: Done. -#> ℹ [2024-03-08 02:37:03.330073]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.33145]: Started. -#> ✔ [2024-03-08 02:37:03.332747]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.334429]: Done. -#> ℹ [2024-03-08 02:37:03.335778]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.337103]: Started. -#> ✔ [2024-03-08 02:37:03.33838]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.340089]: Done. -#> ℹ [2024-03-08 02:37:03.341413]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.342731]: Started. -#> ✔ [2024-03-08 02:37:03.344031]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.345703]: Done. -#> ℹ [2024-03-08 02:37:03.347054]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.348373]: Started. -#> ✔ [2024-03-08 02:37:03.349645]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.35134]: Done. -#> ℹ [2024-03-08 02:37:03.352676]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.353991]: Started. -#> ✔ [2024-03-08 02:37:03.355299]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.357051]: Done. -#> ℹ [2024-03-08 02:37:03.35838]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.359718]: Started. -#> ✔ [2024-03-08 02:37:03.361004]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.362684]: Done. -#> ℹ [2024-03-08 02:37:03.364033]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.365341]: Started. -#> ✔ [2024-03-08 02:37:03.366614]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.368322]: Done. -#> ℹ [2024-03-08 02:37:03.369659]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.370998]: Started. -#> ✔ [2024-03-08 02:37:03.372277]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.373953]: Done. -#> ℹ [2024-03-08 02:37:03.375303]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.376627]: Started. -#> ✔ [2024-03-08 02:37:03.377901]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.379597]: Done. -#> ℹ [2024-03-08 02:37:03.380922]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.382227]: Started. -#> ✔ [2024-03-08 02:37:03.383529]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.385202]: Done. -#> ℹ [2024-03-08 02:37:03.386523]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.387876]: Started. -#> ✔ [2024-03-08 02:37:03.389158]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.390851]: Done. -#> ℹ [2024-03-08 02:37:03.3922]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.39352]: Started. -#> ✔ [2024-03-08 02:37:03.394794]: Batch mode enabled. -#> ! [2024-03-08 02:37:03.396361]: NA result detected from t.test, reporting proportion as p value. -#> ✔ [2024-03-08 02:37:03.397914]: Done. -#> ℹ [2024-03-08 02:37:03.399266]: 0.006 secs elapsed. -#> ℹ [2024-03-08 02:37:03.400582]: Started. -#> ✔ [2024-03-08 02:37:03.401858]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.403576]: Done. -#> ℹ [2024-03-08 02:37:03.404914]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.406231]: Started. -#> ✔ [2024-03-08 02:37:03.407543]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.409209]: Done. -#> ℹ [2024-03-08 02:37:03.410532]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.411872]: Started. -#> ✔ [2024-03-08 02:37:03.413151]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.414852]: Done. -#> ℹ [2024-03-08 02:37:03.416188]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.417499]: Started. -#> ✔ [2024-03-08 02:37:03.418775]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.420471]: Done. -#> ℹ [2024-03-08 02:37:03.421852]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.423219]: Started. -#> ✔ [2024-03-08 02:37:03.424493]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.426173]: Done. -#> ℹ [2024-03-08 02:37:03.427517]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.428849]: Started. -#> ✔ [2024-03-08 02:37:03.43014]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.43184]: Done. -#> ℹ [2024-03-08 02:37:03.433182]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.434494]: Started. -#> ✔ [2024-03-08 02:37:03.435801]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.437473]: Done. -#> ℹ [2024-03-08 02:37:03.4388]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.440156]: Started. -#> ✔ [2024-03-08 02:37:03.441429]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.443118]: Done. -#> ℹ [2024-03-08 02:37:03.444455]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.445764]: Started. -#> ✔ [2024-03-08 02:37:03.447064]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.448745]: Done. -#> ℹ [2024-03-08 02:37:03.450084]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.451437]: Started. -#> ✔ [2024-03-08 02:37:03.452742]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.454427]: Done. -#> ℹ [2024-03-08 02:37:03.455778]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.457104]: Started. -#> ✔ [2024-03-08 02:37:03.458383]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.460067]: Done. -#> ℹ [2024-03-08 02:37:03.461396]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.462729]: Started. -#> ✔ [2024-03-08 02:37:03.464036]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.465719]: Done. -#> ℹ [2024-03-08 02:37:03.467073]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.468391]: Started. -#> ✔ [2024-03-08 02:37:03.469682]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.471375]: Done. -#> ℹ [2024-03-08 02:37:03.47271]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.474024]: Started. -#> ✔ [2024-03-08 02:37:03.475357]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.477056]: Done. -#> ℹ [2024-03-08 02:37:03.478396]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.479745]: Started. -#> ✔ [2024-03-08 02:37:03.481019]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.482695]: Done. -#> ℹ [2024-03-08 02:37:03.484044]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.485352]: Started. -#> ✔ [2024-03-08 02:37:03.486643]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.488347]: Done. -#> ℹ [2024-03-08 02:37:03.489686]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.491051]: Started. -#> ✔ [2024-03-08 02:37:03.492351]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.494036]: Done. -#> ℹ [2024-03-08 02:37:03.495399]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.496725]: Started. -#> ✔ [2024-03-08 02:37:03.498008]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.499716]: Done. -#> ℹ [2024-03-08 02:37:03.501037]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.502353]: Started. -#> ✔ [2024-03-08 02:37:03.503658]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.505332]: Done. -#> ℹ [2024-03-08 02:37:03.506659]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.508003]: Started. -#> ✔ [2024-03-08 02:37:03.509275]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.510966]: Done. -#> ℹ [2024-03-08 02:37:03.512295]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.513607]: Started. -#> ✔ [2024-03-08 02:37:03.514892]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.516556]: Done. -#> ℹ [2024-03-08 02:37:03.517869]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.519201]: Started. -#> ✔ [2024-03-08 02:37:03.52048]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.522138]: Done. -#> ℹ [2024-03-08 02:37:03.5235]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.524815]: Started. -#> ✔ [2024-03-08 02:37:03.526102]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.527786]: Done. -#> ℹ [2024-03-08 02:37:03.529117]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.53045]: Started. -#> ✔ [2024-03-08 02:37:03.531761]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.533444]: Done. -#> ℹ [2024-03-08 02:37:03.534775]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.536118]: Started. -#> ✔ [2024-03-08 02:37:03.537396]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.539088]: Done. -#> ℹ [2024-03-08 02:37:03.540417]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.54174]: Started. -#> ✔ [2024-03-08 02:37:03.543063]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.544844]: Done. -#> ℹ [2024-03-08 02:37:03.546175]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.547517]: Started. -#> ✔ [2024-03-08 02:37:03.548797]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.550474]: Done. -#> ℹ [2024-03-08 02:37:03.551824]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.553169]: Started. -#> ✔ [2024-03-08 02:37:03.55446]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.556169]: Done. -#> ℹ [2024-03-08 02:37:03.557498]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.558825]: Started. -#> ✔ [2024-03-08 02:37:03.560109]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.561788]: Done. -#> ℹ [2024-03-08 02:37:03.563145]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.564466]: Started. -#> ✔ [2024-03-08 02:37:03.565743]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.567424]: Done. -#> ℹ [2024-03-08 02:37:03.568763]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.570082]: Started. -#> ✔ [2024-03-08 02:37:03.571387]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.57306]: Done. -#> ℹ [2024-03-08 02:37:03.574384]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.575746]: Started. -#> ✔ [2024-03-08 02:37:03.577025]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.578691]: Done. -#> ℹ [2024-03-08 02:37:03.580075]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.581396]: Started. -#> ✔ [2024-03-08 02:37:03.582671]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.584378]: Done. -#> ℹ [2024-03-08 02:37:03.585711]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.587046]: Started. -#> ✔ [2024-03-08 02:37:03.588329]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.589994]: Done. -#> ℹ [2024-03-08 02:37:03.591385]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.592707]: Started. -#> ✔ [2024-03-08 02:37:03.594002]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.595727]: Done. -#> ℹ [2024-03-08 02:37:03.597069]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.59841]: Started. -#> ✔ [2024-03-08 02:37:03.599725]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.601442]: Done. -#> ℹ [2024-03-08 02:37:03.602779]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.60412]: Started. -#> ✔ [2024-03-08 02:37:03.605399]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.607093]: Done. -#> ℹ [2024-03-08 02:37:03.60843]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.609788]: Started. -#> ✔ [2024-03-08 02:37:03.611109]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.612812]: Done. -#> ℹ [2024-03-08 02:37:03.614162]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.615535]: Started. -#> ✔ [2024-03-08 02:37:03.616841]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.618532]: Done. -#> ℹ [2024-03-08 02:37:03.619915]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.62127]: Started. -#> ✔ [2024-03-08 02:37:03.62258]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.624311]: Done. -#> ℹ [2024-03-08 02:37:03.625698]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.627046]: Started. -#> ✔ [2024-03-08 02:37:03.628347]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.630048]: Done. -#> ℹ [2024-03-08 02:37:03.631443]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.632804]: Started. -#> ✔ [2024-03-08 02:37:03.634099]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.635843]: Done. -#> ℹ [2024-03-08 02:37:03.63718]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.638507]: Started. -#> ✔ [2024-03-08 02:37:03.63983]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.641693]: Done. -#> ℹ [2024-03-08 02:37:03.643135]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.644521]: Started. -#> ✔ [2024-03-08 02:37:03.645866]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.647671]: Done. -#> ℹ [2024-03-08 02:37:03.649075]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.650491]: Started. -#> ✔ [2024-03-08 02:37:03.651873]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.653669]: Done. -#> ℹ [2024-03-08 02:37:03.655091]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.65649]: Started. -#> ✔ [2024-03-08 02:37:03.657845]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.659663]: Done. -#> ℹ [2024-03-08 02:37:03.661085]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.662474]: Started. -#> ✔ [2024-03-08 02:37:03.663857]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.665609]: Done. -#> ℹ [2024-03-08 02:37:03.667024]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.668411]: Started. -#> ✔ [2024-03-08 02:37:03.669771]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.671535]: Done. -#> ℹ [2024-03-08 02:37:03.672948]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.674325]: Started. -#> ✔ [2024-03-08 02:37:03.675677]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.677406]: Done. -#> ℹ [2024-03-08 02:37:03.678784]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.680167]: Started. -#> ✔ [2024-03-08 02:37:03.681495]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.683262]: Done. -#> ℹ [2024-03-08 02:37:03.684644]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.686012]: Started. -#> ✔ [2024-03-08 02:37:03.687383]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.689217]: Done. -#> ℹ [2024-03-08 02:37:03.690595]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.692002]: Started. -#> ✔ [2024-03-08 02:37:03.693346]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.695114]: Done. -#> ℹ [2024-03-08 02:37:03.696494]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.697856]: Started. -#> ✔ [2024-03-08 02:37:03.699207]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.700924]: Done. -#> ℹ [2024-03-08 02:37:03.702297]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.703701]: Started. -#> ✔ [2024-03-08 02:37:03.705032]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.706781]: Done. -#> ℹ [2024-03-08 02:37:03.708193]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.709569]: Started. -#> ✔ [2024-03-08 02:37:03.710951]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.712709]: Done. -#> ℹ [2024-03-08 02:37:03.714101]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.715496]: Started. -#> ✔ [2024-03-08 02:37:03.71682]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.718565]: Done. -#> ℹ [2024-03-08 02:37:03.719982]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.721355]: Started. -#> ✔ [2024-03-08 02:37:03.722677]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.724444]: Done. -#> ℹ [2024-03-08 02:37:03.725821]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.727228]: Started. -#> ✔ [2024-03-08 02:37:03.728569]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.73031]: Done. -#> ℹ [2024-03-08 02:37:03.731712]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.733099]: Started. -#> ✔ [2024-03-08 02:37:03.73444]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.73622]: Done. -#> ℹ [2024-03-08 02:37:03.737597]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.738991]: Started. -#> ✔ [2024-03-08 02:37:03.74032]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.742061]: Done. -#> ℹ [2024-03-08 02:37:03.743462]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.744832]: Started. -#> ✔ [2024-03-08 02:37:03.746156]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.747921]: Done. -#> ℹ [2024-03-08 02:37:03.749317]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.750703]: Started. -#> ✔ [2024-03-08 02:37:03.752074]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.753827]: Done. -#> ℹ [2024-03-08 02:37:03.755253]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.756629]: Started. -#> ✔ [2024-03-08 02:37:03.757973]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.759741]: Done. -#> ℹ [2024-03-08 02:37:03.76114]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.762525]: Started. -#> ✔ [2024-03-08 02:37:03.763882]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.765617]: Done. -#> ℹ [2024-03-08 02:37:03.767023]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.768392]: Started. -#> ✔ [2024-03-08 02:37:03.769745]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.771539]: Done. -#> ℹ [2024-03-08 02:37:03.772931]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.774311]: Started. -#> ✔ [2024-03-08 02:37:03.775666]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.777404]: Done. -#> ℹ [2024-03-08 02:37:03.778797]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.780218]: Started. -#> ✔ [2024-03-08 02:37:03.781555]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.783335]: Done. -#> ℹ [2024-03-08 02:37:03.784712]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.786083]: Started. -#> ✔ [2024-03-08 02:37:03.787447]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.789319]: Done. -#> ℹ [2024-03-08 02:37:03.790714]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:37:03.792134]: Started. -#> ✔ [2024-03-08 02:37:03.793475]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.795238]: Done. -#> ℹ [2024-03-08 02:37:03.79664]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.798005]: Started. -#> ✔ [2024-03-08 02:37:03.799362]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.801097]: Done. -#> ℹ [2024-03-08 02:37:03.802471]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.803877]: Started. -#> ✔ [2024-03-08 02:37:03.805228]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.806991]: Done. -#> ℹ [2024-03-08 02:37:03.808371]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.809811]: Started. -#> ✔ [2024-03-08 02:37:03.811181]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.812936]: Done. -#> ℹ [2024-03-08 02:37:03.814322]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.815716]: Started. -#> ✔ [2024-03-08 02:37:03.817051]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.81879]: Done. -#> ℹ [2024-03-08 02:37:03.820205]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.821583]: Started. -#> ✔ [2024-03-08 02:37:03.822955]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.824696]: Done. -#> ℹ [2024-03-08 02:37:03.826078]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.827488]: Started. -#> ✔ [2024-03-08 02:37:03.828825]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.830578]: Done. -#> ℹ [2024-03-08 02:37:03.831987]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.833369]: Started. -#> ✔ [2024-03-08 02:37:03.834709]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.836481]: Done. -#> ℹ [2024-03-08 02:37:03.837869]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.83927]: Started. -#> ✔ [2024-03-08 02:37:03.840601]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.84234]: Done. -#> ℹ [2024-03-08 02:37:03.843768]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.845145]: Started. -#> ✔ [2024-03-08 02:37:03.846478]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.848239]: Done. -#> ℹ [2024-03-08 02:37:03.84962]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.851014]: Started. -#> ✔ [2024-03-08 02:37:03.852347]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.864356]: Done. -#> ℹ [2024-03-08 02:37:03.865713]: 0.015 secs elapsed. -#> ℹ [2024-03-08 02:37:03.867075]: Started. -#> ✔ [2024-03-08 02:37:03.868385]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.870076]: Done. -#> ℹ [2024-03-08 02:37:03.871423]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.872743]: Started. -#> ✔ [2024-03-08 02:37:03.874036]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.875745]: Done. -#> ℹ [2024-03-08 02:37:03.877073]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.878391]: Started. -#> ✔ [2024-03-08 02:37:03.879705]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.881433]: Done. -#> ℹ [2024-03-08 02:37:03.882773]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.884118]: Started. -#> ✔ [2024-03-08 02:37:03.885397]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.887104]: Done. -#> ℹ [2024-03-08 02:37:03.888439]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.88976]: Started. -#> ✔ [2024-03-08 02:37:03.891103]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.892813]: Done. -#> ℹ [2024-03-08 02:37:03.894161]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.895509]: Started. -#> ✔ [2024-03-08 02:37:03.8968]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.898478]: Done. -#> ℹ [2024-03-08 02:37:03.899832]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.901155]: Started. -#> ✔ [2024-03-08 02:37:03.902441]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.904141]: Done. -#> ℹ [2024-03-08 02:37:03.90547]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.906802]: Started. -#> ✔ [2024-03-08 02:37:03.908103]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.909791]: Done. -#> ℹ [2024-03-08 02:37:03.91115]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.912494]: Started. -#> ✔ [2024-03-08 02:37:03.913807]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.91551]: Done. -#> ℹ [2024-03-08 02:37:03.916853]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.918188]: Started. -#> ✔ [2024-03-08 02:37:03.919491]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.921181]: Done. -#> ℹ [2024-03-08 02:37:03.922512]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.923865]: Started. -#> ✔ [2024-03-08 02:37:03.925156]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.926869]: Done. -#> ℹ [2024-03-08 02:37:03.928207]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.929549]: Started. -#> ✔ [2024-03-08 02:37:03.930859]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.932539]: Done. -#> ℹ [2024-03-08 02:37:03.93387]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.935214]: Started. -#> ✔ [2024-03-08 02:37:03.936502]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.938189]: Done. -#> ℹ [2024-03-08 02:37:03.939541]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.940861]: Started. -#> ✔ [2024-03-08 02:37:03.94214]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.943845]: Done. -#> ℹ [2024-03-08 02:37:03.945183]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.946507]: Started. -#> ✔ [2024-03-08 02:37:03.947822]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.949504]: Done. -#> ℹ [2024-03-08 02:37:03.950857]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.952191]: Started. -#> ✔ [2024-03-08 02:37:03.953486]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.955192]: Done. -#> ℹ [2024-03-08 02:37:03.95653]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.957853]: Started. -#> ✔ [2024-03-08 02:37:03.959156]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.960831]: Done. -#> ℹ [2024-03-08 02:37:03.962164]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.963544]: Started. -#> ✔ [2024-03-08 02:37:03.964834]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.966512]: Done. -#> ℹ [2024-03-08 02:37:03.967867]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.969198]: Started. -#> ✔ [2024-03-08 02:37:03.970494]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.972231]: Done. -#> ℹ [2024-03-08 02:37:03.97358]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:03.974929]: Started. -#> ✔ [2024-03-08 02:37:03.976221]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:03.977912]: Done. -#> ℹ [2024-03-08 02:37:03.979265]: 0.004 secs elapsed. -#> ℹ 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[2024-03-08 02:37:04.066132]: Started. -#> ✔ [2024-03-08 02:37:04.067499]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.06921]: Done. -#> ℹ [2024-03-08 02:37:04.07056]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.071922]: Started. -#> ✔ [2024-03-08 02:37:04.073222]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.074939]: Done. -#> ℹ [2024-03-08 02:37:04.076285]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.077613]: Started. -#> ✔ [2024-03-08 02:37:04.078926]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.080626]: Done. -#> ℹ [2024-03-08 02:37:04.081978]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.083337]: Started. -#> ✔ [2024-03-08 02:37:04.084637]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.086318]: Done. -#> ℹ [2024-03-08 02:37:04.087689]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.08902]: Started. -#> ✔ [2024-03-08 02:37:04.090306]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.092016]: Done. -#> ℹ [2024-03-08 02:37:04.093365]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.094697]: Started. -#> ✔ [2024-03-08 02:37:04.096009]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.097692]: Done. -#> ℹ [2024-03-08 02:37:04.099063]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.100498]: Started. -#> ✔ [2024-03-08 02:37:04.101876]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.103633]: Done. -#> ℹ [2024-03-08 02:37:04.104982]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.106318]: Started. -#> ✔ [2024-03-08 02:37:04.107658]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.109355]: Done. -#> ℹ [2024-03-08 02:37:04.110741]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.112116]: Started. -#> ✔ [2024-03-08 02:37:04.113405]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.115146]: Done. -#> ℹ [2024-03-08 02:37:04.116495]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.117825]: Started. -#> ✔ [2024-03-08 02:37:04.119161]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.120858]: Done. -#> ℹ [2024-03-08 02:37:04.122208]: 0.004 secs elapsed. -#> ℹ 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[2024-03-08 02:37:04.152069]: Started. -#> ✔ [2024-03-08 02:37:04.15337]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.155065]: Done. -#> ℹ [2024-03-08 02:37:04.156399]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.157741]: Started. -#> ✔ [2024-03-08 02:37:04.159061]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.160774]: Done. -#> ℹ [2024-03-08 02:37:04.162132]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.163497]: Started. -#> ✔ [2024-03-08 02:37:04.164784]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.166486]: Done. -#> ℹ [2024-03-08 02:37:04.167848]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.169236]: Started. -#> ✔ [2024-03-08 02:37:04.170536]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.172253]: Done. -#> ℹ [2024-03-08 02:37:04.173603]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.174956]: Started. -#> ✔ [2024-03-08 02:37:04.17625]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.177943]: Done. -#> ℹ [2024-03-08 02:37:04.179321]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.180664]: Started. -#> ✔ [2024-03-08 02:37:04.181956]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.183666]: Done. -#> ℹ [2024-03-08 02:37:04.185004]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.18633]: Started. -#> ✔ [2024-03-08 02:37:04.187636]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.189395]: Done. -#> ℹ [2024-03-08 02:37:04.190735]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.192109]: Started. -#> ✔ [2024-03-08 02:37:04.193421]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.195121]: Done. -#> ℹ [2024-03-08 02:37:04.196468]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.197788]: Started. -#> ✔ [2024-03-08 02:37:04.199098]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.200781]: Done. -#> ℹ [2024-03-08 02:37:04.202132]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.203494]: Started. -#> ✔ [2024-03-08 02:37:04.204785]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.206468]: Done. -#> ℹ [2024-03-08 02:37:04.207831]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.209178]: Started. -#> ✔ [2024-03-08 02:37:04.210466]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.212173]: Done. -#> ℹ [2024-03-08 02:37:04.21352]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.214865]: Started. -#> ✔ [2024-03-08 02:37:04.216255]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.21796]: Done. -#> ℹ [2024-03-08 02:37:04.21932]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.220657]: Started. -#> ✔ [2024-03-08 02:37:04.221949]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.223667]: Done. -#> ℹ [2024-03-08 02:37:04.225017]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.226351]: Started. -#> ✔ [2024-03-08 02:37:04.227691]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.229393]: Done. -#> ℹ [2024-03-08 02:37:04.230778]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.232151]: Started. -#> ✔ [2024-03-08 02:37:04.23347]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.235183]: Done. -#> ℹ [2024-03-08 02:37:04.236532]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:37:04.237885]: Started. -#> ✔ [2024-03-08 02:37:04.239218]: Batch mode enabled. -#> ✔ [2024-03-08 02:37:04.240937]: Done. -#> ℹ [2024-03-08 02:37:04.242301]: 0.004 secs elapsed. -#> ✔ [2024-03-08 02:37:04.243694]: Done. -#> ℹ [2024-03-08 02:37:04.245018]: Cleaning results... -#> ✔ [2024-03-08 02:37:05.583434]: Outputing. -#> ℹ [2024-03-08 02:37:05.585817]: Total 3.047 mins elapsed. -#> ℹ [2024-03-08 02:37:05.587574]: Started. -#> ✔ [2024-03-08 02:37:05.590144]: NULL sample detected, aggregate mode enabled. -#> ℹ [2024-03-08 02:37:05.591537]: The summarized values will be stored in 'summary' element of result ggplot2 object. -#> ℹ [2024-03-08 02:37:05.61712]: Plotting. -#> ℹ [2024-03-08 02:37:05.665723]: 0.078 secs elapsed. -#> ℹ [2024-03-08 02:37:05.667283]: Started. -#> ℹ [2024-03-08 02:37:05.670609]: Plotting. -#> ℹ [2024-03-08 02:37:05.714306]: 0.047 secs elapsed. -#> ℹ [2024-03-08 02:37:05.716068]: Started. -#> ℹ [2024-03-08 02:37:05.720316]: Plotting. -#> ℹ [2024-03-08 02:37:05.764601]: 0.048 secs elapsed. -#> ℹ [2024-03-08 02:37:05.766611]: Started. -#> ✔ [2024-03-08 02:37:05.76931]: NULL sample detected, aggregate mode enabled. -#> ℹ [2024-03-08 02:37:05.770705]: The summarized values will be stored in 'summary' element of result ggplot2 object. -#> ℹ [2024-03-08 02:37:05.783326]: Plotting. -#> ℹ [2024-03-08 02:37:05.826596]: 0.06 secs elapsed. -#> ℹ [2024-03-08 02:37:05.828205]: Started. -#> ℹ [2024-03-08 02:37:05.8314]: Plotting. -#> ℹ [2024-03-08 02:37:05.876751]: 0.049 secs elapsed. -#> ℹ [2024-03-08 02:37:05.878666]: Started. -#> ℹ [2024-03-08 02:37:05.896605]: Plotting. -#> ℹ [2024-03-08 02:37:05.936779]: 0.058 secs elapsed. -#> ℹ [2024-03-08 02:37:05.938351]: Started. -#> ℹ [2024-03-08 02:37:05.954111]: Plotting. -#> ℹ [2024-03-08 02:37:06.006807]: 0.068 secs elapsed. -#> ℹ [2024-03-08 02:37:06.008533]: Started. -#> ℹ [2024-03-08 02:37:06.046561]: Plotting. -#> ℹ [2024-03-08 02:37:06.087126]: 0.079 secs elapsed. -#> ℹ [2024-03-08 02:37:06.088679]: Started. -#> ℹ [2024-03-08 02:37:06.107008]: Plotting. -#> ℹ [2024-03-08 02:37:06.14752]: 0.059 secs elapsed. +#> 6.722 0.056 6.778 +#> ℹ [2024-03-13 10:48:30.799862]: Batch Bootstrap Signature Exposure Analysis Started. +#> ℹ [2024-03-13 10:48:30.801665]: Samples to be filtered out: TCGA-AB-2825,TCGA-AB-2834,TCGA-AB-2866,TCGA-AB-2873,TCGA-AB-2880,TCGA-AB-2883,TCGA-AB-2892,TCGA-AB-2896,TCGA-AB-2903,TCGA-AB-2918,TCGA-AB-2933,TCGA-AB-2948,TCGA-AB-2954 +#> ℹ [2024-03-13 10:48:30.803106]: Finding optimal exposures (&errors) for different methods. +#> ℹ [2024-03-13 10:48:30.804568]: Calling method `QP`. +#> ℹ [2024-03-13 10:48:30.807838]: Started. +#> ℹ [2024-03-13 10:48:30.80918]: Signature index not detected. +#> ✔ [2024-03-13 10:48:30.810529]: Signature object detected. +#> ✔ [2024-03-13 10:48:30.811922]: Database and index checked. +#> ✔ [2024-03-13 10:48:30.813348]: Signature normalized. +#> ℹ [2024-03-13 10:48:30.814682]: Checking row number for catalog matrix and signature matrix. +#> ✔ [2024-03-13 10:48:30.816035]: Checked. +#> ℹ [2024-03-13 10:48:30.817352]: Checking rownames for catalog matrix and signature matrix. +#> ✔ [2024-03-13 10:48:30.818673]: Checked. +#> ✔ [2024-03-13 10:48:30.820034]: Method 'QP' detected. +#> ✔ [2024-03-13 10:48:30.82137]: Corresponding function generated. +#> ℹ [2024-03-13 10:48:30.822682]: Calling function. +#> ℹ [2024-03-13 10:48:30.824826]: Fitting sample: TCGA-AB-2802 +#> ℹ [2024-03-13 10:48:30.826288]: Fitting sample: TCGA-AB-2803 +#> ℹ [2024-03-13 10:48:30.827714]: Fitting sample: TCGA-AB-2804 +#> ℹ [2024-03-13 10:48:30.829106]: Fitting sample: TCGA-AB-2805 +#> ℹ [2024-03-13 10:48:30.830505]: Fitting sample: TCGA-AB-2806 +#> ℹ [2024-03-13 10:48:30.831959]: Fitting sample: TCGA-AB-2807 +#> ℹ [2024-03-13 10:48:30.833358]: Fitting sample: TCGA-AB-2808 +#> ℹ [2024-03-13 10:48:30.834749]: Fitting sample: TCGA-AB-2809 +#> ℹ [2024-03-13 10:48:30.836165]: Fitting sample: TCGA-AB-2810 +#> ℹ [2024-03-13 10:48:30.837558]: Fitting sample: TCGA-AB-2812 +#> ℹ [2024-03-13 10:48:30.83894]: Fitting sample: TCGA-AB-2813 +#> ℹ [2024-03-13 10:48:30.840361]: Fitting sample: TCGA-AB-2814 +#> ℹ [2024-03-13 10:48:30.841776]: Fitting sample: TCGA-AB-2816 +#> ℹ [2024-03-13 10:48:30.843155]: Fitting sample: TCGA-AB-2817 +#> ℹ [2024-03-13 10:48:30.844571]: Fitting sample: TCGA-AB-2818 +#> ℹ [2024-03-13 10:48:30.845967]: Fitting sample: TCGA-AB-2819 +#> ℹ [2024-03-13 10:48:30.847394]: Fitting sample: TCGA-AB-2820 +#> ℹ [2024-03-13 10:48:30.848784]: Fitting sample: TCGA-AB-2821 +#> ℹ [2024-03-13 10:48:30.850185]: Fitting sample: TCGA-AB-2822 +#> ℹ [2024-03-13 10:48:30.851603]: Fitting sample: TCGA-AB-2824 +#> ℹ [2024-03-13 10:48:30.852997]: Fitting sample: TCGA-AB-2826 +#> ℹ [2024-03-13 10:48:30.854386]: Fitting sample: TCGA-AB-2827 +#> ℹ [2024-03-13 10:48:30.855832]: Fitting sample: TCGA-AB-2828 +#> ℹ [2024-03-13 10:48:30.857234]: Fitting sample: TCGA-AB-2829 +#> ℹ [2024-03-13 10:48:30.858634]: Fitting sample: TCGA-AB-2830 +#> ℹ [2024-03-13 10:48:30.860049]: Fitting sample: TCGA-AB-2831 +#> ℹ [2024-03-13 10:48:30.861454]: Fitting sample: TCGA-AB-2832 +#> ℹ [2024-03-13 10:48:30.862847]: Fitting sample: TCGA-AB-2833 +#> ℹ [2024-03-13 10:48:30.864254]: Fitting sample: TCGA-AB-2835 +#> ℹ [2024-03-13 10:48:30.865627]: Fitting sample: TCGA-AB-2836 +#> ℹ [2024-03-13 10:48:30.867034]: Fitting sample: TCGA-AB-2838 +#> ℹ [2024-03-13 10:48:30.868504]: Fitting sample: TCGA-AB-2839 +#> ℹ [2024-03-13 10:48:30.869888]: Fitting sample: TCGA-AB-2841 +#> ℹ [2024-03-13 10:48:30.871297]: Fitting sample: TCGA-AB-2842 +#> ℹ [2024-03-13 10:48:30.87269]: Fitting sample: TCGA-AB-2843 +#> ℹ [2024-03-13 10:48:30.874075]: Fitting sample: TCGA-AB-2844 +#> ℹ [2024-03-13 10:48:30.875483]: Fitting sample: TCGA-AB-2845 +#> ℹ [2024-03-13 10:48:30.876861]: Fitting sample: TCGA-AB-2846 +#> ℹ [2024-03-13 10:48:30.878256]: Fitting sample: TCGA-AB-2847 +#> ℹ [2024-03-13 10:48:30.879667]: Fitting sample: TCGA-AB-2849 +#> ℹ [2024-03-13 10:48:30.881047]: Fitting sample: TCGA-AB-2850 +#> ℹ [2024-03-13 10:48:30.882433]: Fitting sample: TCGA-AB-2851 +#> ℹ [2024-03-13 10:48:30.883872]: Fitting sample: TCGA-AB-2853 +#> ℹ [2024-03-13 10:48:30.885279]: Fitting sample: TCGA-AB-2854 +#> ℹ [2024-03-13 10:48:30.88668]: Fitting sample: TCGA-AB-2855 +#> ℹ [2024-03-13 10:48:30.888106]: Fitting sample: TCGA-AB-2857 +#> ℹ [2024-03-13 10:48:30.889502]: Fitting sample: TCGA-AB-2858 +#> ℹ [2024-03-13 10:48:30.890888]: Fitting sample: TCGA-AB-2859 +#> ℹ [2024-03-13 10:48:30.892309]: Fitting sample: TCGA-AB-2860 +#> ℹ [2024-03-13 10:48:30.893691]: Fitting sample: TCGA-AB-2861 +#> ℹ [2024-03-13 10:48:30.895073]: Fitting sample: TCGA-AB-2862 +#> ℹ [2024-03-13 10:48:30.896488]: Fitting sample: TCGA-AB-2863 +#> ℹ [2024-03-13 10:48:30.897871]: Fitting sample: TCGA-AB-2864 +#> ℹ [2024-03-13 10:48:30.899273]: Fitting sample: TCGA-AB-2865 +#> ℹ [2024-03-13 10:48:30.900663]: Fitting sample: TCGA-AB-2867 +#> ℹ [2024-03-13 10:48:30.902046]: Fitting sample: TCGA-AB-2868 +#> ℹ [2024-03-13 10:48:30.903447]: Fitting sample: TCGA-AB-2869 +#> ℹ [2024-03-13 10:48:30.904837]: Fitting sample: TCGA-AB-2870 +#> ℹ [2024-03-13 10:48:30.906224]: Fitting sample: TCGA-AB-2871 +#> ℹ [2024-03-13 10:48:30.907637]: Fitting sample: TCGA-AB-2872 +#> ℹ [2024-03-13 10:48:30.909029]: Fitting sample: TCGA-AB-2874 +#> ℹ [2024-03-13 10:48:30.910415]: Fitting sample: TCGA-AB-2875 +#> ℹ [2024-03-13 10:48:30.911846]: Fitting sample: TCGA-AB-2876 +#> ℹ [2024-03-13 10:48:30.913231]: Fitting sample: TCGA-AB-2877 +#> ℹ [2024-03-13 10:48:30.914606]: Fitting sample: TCGA-AB-2878 +#> ℹ [2024-03-13 10:48:30.916017]: Fitting sample: TCGA-AB-2879 +#> ℹ [2024-03-13 10:48:30.917394]: Fitting sample: TCGA-AB-2881 +#> ℹ [2024-03-13 10:48:30.918784]: Fitting sample: TCGA-AB-2882 +#> ℹ [2024-03-13 10:48:30.920204]: Fitting sample: TCGA-AB-2884 +#> ℹ [2024-03-13 10:48:30.921611]: Fitting sample: TCGA-AB-2885 +#> ℹ [2024-03-13 10:48:30.923004]: Fitting sample: TCGA-AB-2886 +#> ℹ [2024-03-13 10:48:30.924439]: Fitting sample: TCGA-AB-2887 +#> ℹ [2024-03-13 10:48:30.925827]: Fitting sample: TCGA-AB-2888 +#> ℹ [2024-03-13 10:48:30.927209]: Fitting sample: TCGA-AB-2889 +#> ℹ [2024-03-13 10:48:30.928622]: Fitting sample: TCGA-AB-2890 +#> ℹ [2024-03-13 10:48:30.930004]: Fitting sample: TCGA-AB-2891 +#> ℹ [2024-03-13 10:48:30.931421]: Fitting sample: TCGA-AB-2894 +#> ℹ [2024-03-13 10:48:30.932824]: Fitting sample: TCGA-AB-2895 +#> ℹ [2024-03-13 10:48:30.93421]: Fitting sample: TCGA-AB-2897 +#> ℹ [2024-03-13 10:48:30.93562]: Fitting sample: TCGA-AB-2898 +#> ℹ [2024-03-13 10:48:30.937007]: Fitting sample: TCGA-AB-2899 +#> ℹ [2024-03-13 10:48:30.938393]: Fitting sample: TCGA-AB-2900 +#> ℹ [2024-03-13 10:48:30.939823]: Fitting sample: TCGA-AB-2901 +#> ℹ [2024-03-13 10:48:30.941224]: Fitting sample: TCGA-AB-2904 +#> ℹ [2024-03-13 10:48:30.942617]: Fitting sample: TCGA-AB-2905 +#> ℹ [2024-03-13 10:48:30.944029]: Fitting sample: TCGA-AB-2906 +#> ℹ [2024-03-13 10:48:30.945412]: Fitting sample: TCGA-AB-2907 +#> ℹ [2024-03-13 10:48:30.946808]: Fitting sample: TCGA-AB-2908 +#> ℹ [2024-03-13 10:48:30.948218]: Fitting sample: TCGA-AB-2910 +#> ℹ [2024-03-13 10:48:30.949598]: Fitting sample: TCGA-AB-2911 +#> ℹ [2024-03-13 10:48:30.950983]: Fitting sample: TCGA-AB-2912 +#> ℹ [2024-03-13 10:48:30.952399]: Fitting sample: TCGA-AB-2913 +#> ℹ [2024-03-13 10:48:30.953786]: Fitting sample: TCGA-AB-2914 +#> ℹ [2024-03-13 10:48:30.955167]: Fitting sample: TCGA-AB-2915 +#> ℹ [2024-03-13 10:48:30.956586]: Fitting sample: TCGA-AB-2916 +#> ℹ [2024-03-13 10:48:30.957992]: Fitting sample: TCGA-AB-2917 +#> ℹ [2024-03-13 10:48:30.959402]: Fitting sample: TCGA-AB-2919 +#> ℹ [2024-03-13 10:48:30.960802]: Fitting sample: TCGA-AB-2920 +#> ℹ [2024-03-13 10:48:30.962214]: Fitting sample: TCGA-AB-2921 +#> ℹ [2024-03-13 10:48:30.963623]: Fitting sample: TCGA-AB-2922 +#> ℹ [2024-03-13 10:48:30.96501]: Fitting sample: TCGA-AB-2923 +#> ℹ [2024-03-13 10:48:30.966413]: Fitting sample: TCGA-AB-2924 +#> ℹ [2024-03-13 10:48:30.967845]: Fitting sample: TCGA-AB-2925 +#> ℹ [2024-03-13 10:48:30.969237]: Fitting sample: TCGA-AB-2926 +#> ℹ [2024-03-13 10:48:30.970619]: Fitting sample: TCGA-AB-2927 +#> ℹ [2024-03-13 10:48:30.972035]: Fitting sample: TCGA-AB-2928 +#> ℹ [2024-03-13 10:48:30.973426]: Fitting sample: TCGA-AB-2929 +#> ℹ [2024-03-13 10:48:30.974818]: Fitting sample: TCGA-AB-2930 +#> ℹ [2024-03-13 10:48:30.976248]: Fitting sample: TCGA-AB-2931 +#> ℹ [2024-03-13 10:48:30.977659]: Fitting sample: TCGA-AB-2932 +#> ℹ [2024-03-13 10:48:30.979059]: Fitting sample: TCGA-AB-2934 +#> ℹ [2024-03-13 10:48:30.980508]: Fitting sample: TCGA-AB-2935 +#> ℹ [2024-03-13 10:48:30.981914]: Fitting sample: TCGA-AB-2936 +#> ℹ [2024-03-13 10:48:30.983318]: Fitting sample: TCGA-AB-2937 +#> ℹ [2024-03-13 10:48:30.984713]: Fitting sample: TCGA-AB-2938 +#> ℹ [2024-03-13 10:48:30.986096]: Fitting sample: TCGA-AB-2939 +#> ℹ [2024-03-13 10:48:30.98752]: Fitting sample: TCGA-AB-2940 +#> ℹ [2024-03-13 10:48:30.988911]: Fitting sample: TCGA-AB-2941 +#> ℹ [2024-03-13 10:48:30.990299]: Fitting sample: TCGA-AB-2943 +#> ℹ [2024-03-13 10:48:30.991732]: Fitting sample: TCGA-AB-2945 +#> ℹ [2024-03-13 10:48:30.993125]: Fitting sample: TCGA-AB-2946 +#> ℹ [2024-03-13 10:48:30.994531]: Fitting sample: TCGA-AB-2947 +#> ℹ [2024-03-13 10:48:30.995939]: Fitting sample: TCGA-AB-2949 +#> ℹ [2024-03-13 10:48:30.997321]: Fitting sample: TCGA-AB-2950 +#> ℹ [2024-03-13 10:48:31.009848]: Fitting sample: TCGA-AB-2952 +#> ℹ [2024-03-13 10:48:31.011318]: Fitting sample: TCGA-AB-2955 +#> ℹ [2024-03-13 10:48:31.012742]: Fitting sample: TCGA-AB-2956 +#> ℹ [2024-03-13 10:48:31.014132]: Fitting sample: TCGA-AB-2957 +#> ℹ [2024-03-13 10:48:31.015532]: Fitting sample: TCGA-AB-2959 +#> ℹ [2024-03-13 10:48:31.016974]: Fitting sample: TCGA-AB-2963 +#> ℹ [2024-03-13 10:48:31.018379]: Fitting sample: TCGA-AB-2964 +#> ℹ [2024-03-13 10:48:31.019806]: Fitting sample: TCGA-AB-2965 +#> ℹ [2024-03-13 10:48:31.021215]: Fitting sample: TCGA-AB-2966 +#> ℹ [2024-03-13 10:48:31.02264]: Fitting sample: TCGA-AB-2967 +#> ℹ [2024-03-13 10:48:31.024052]: Fitting sample: TCGA-AB-2968 +#> ℹ [2024-03-13 10:48:31.025478]: Fitting sample: TCGA-AB-2970 +#> ℹ [2024-03-13 10:48:31.026876]: Fitting sample: TCGA-AB-2971 +#> ℹ [2024-03-13 10:48:31.028288]: Fitting sample: TCGA-AB-2972 +#> ℹ [2024-03-13 10:48:31.029672]: Fitting sample: TCGA-AB-2973 +#> ℹ [2024-03-13 10:48:31.031057]: Fitting sample: TCGA-AB-2974 +#> ℹ [2024-03-13 10:48:31.032475]: Fitting sample: TCGA-AB-2975 +#> ℹ [2024-03-13 10:48:31.033864]: Fitting sample: TCGA-AB-2976 +#> ℹ [2024-03-13 10:48:31.035247]: Fitting sample: TCGA-AB-2977 +#> ℹ [2024-03-13 10:48:31.036654]: Fitting sample: TCGA-AB-2978 +#> ℹ [2024-03-13 10:48:31.038036]: Fitting sample: TCGA-AB-2979 +#> ℹ [2024-03-13 10:48:31.03946]: Fitting sample: TCGA-AB-2980 +#> ℹ [2024-03-13 10:48:31.040849]: Fitting sample: TCGA-AB-2981 +#> ℹ [2024-03-13 10:48:31.042254]: Fitting sample: TCGA-AB-2982 +#> ℹ [2024-03-13 10:48:31.043682]: Fitting sample: TCGA-AB-2983 +#> ℹ [2024-03-13 10:48:31.045069]: Fitting sample: TCGA-AB-2984 +#> ℹ [2024-03-13 10:48:31.046449]: Fitting sample: TCGA-AB-2985 +#> ℹ [2024-03-13 10:48:31.047881]: Fitting sample: TCGA-AB-2986 +#> ℹ [2024-03-13 10:48:31.049341]: Fitting sample: TCGA-AB-2987 +#> ℹ [2024-03-13 10:48:31.050745]: Fitting sample: TCGA-AB-2988 +#> ℹ [2024-03-13 10:48:31.052161]: Fitting sample: TCGA-AB-2989 +#> ℹ [2024-03-13 10:48:31.053543]: Fitting sample: TCGA-AB-2990 +#> ℹ [2024-03-13 10:48:31.054925]: Fitting sample: TCGA-AB-2991 +#> ℹ [2024-03-13 10:48:31.056361]: Fitting sample: TCGA-AB-2992 +#> ℹ [2024-03-13 10:48:31.057746]: Fitting sample: TCGA-AB-2993 +#> ℹ [2024-03-13 10:48:31.05914]: Fitting sample: TCGA-AB-2994 +#> ℹ [2024-03-13 10:48:31.060569]: Fitting sample: TCGA-AB-2995 +#> ℹ [2024-03-13 10:48:31.061971]: Fitting sample: TCGA-AB-2996 +#> ℹ [2024-03-13 10:48:31.063381]: Fitting sample: TCGA-AB-2997 +#> ℹ [2024-03-13 10:48:31.064784]: Fitting sample: TCGA-AB-2998 +#> ℹ [2024-03-13 10:48:31.066194]: Fitting sample: TCGA-AB-2999 +#> ℹ [2024-03-13 10:48:31.067609]: Fitting sample: TCGA-AB-3000 +#> ℹ [2024-03-13 10:48:31.068998]: Fitting sample: TCGA-AB-3001 +#> ℹ [2024-03-13 10:48:31.070377]: Fitting sample: TCGA-AB-3002 +#> ℹ [2024-03-13 10:48:31.071809]: Fitting sample: TCGA-AB-3005 +#> ℹ [2024-03-13 10:48:31.073231]: Fitting sample: TCGA-AB-3006 +#> ℹ [2024-03-13 10:48:31.074645]: Fitting sample: TCGA-AB-3007 +#> ℹ [2024-03-13 10:48:31.07607]: Fitting sample: TCGA-AB-3008 +#> ℹ [2024-03-13 10:48:31.077458]: Fitting sample: TCGA-AB-3009 +#> ℹ [2024-03-13 10:48:31.078855]: Fitting sample: TCGA-AB-3011 +#> ℹ [2024-03-13 10:48:31.080265]: Fitting sample: TCGA-AB-3012 +#> ✔ [2024-03-13 10:48:31.08169]: Done. +#> ℹ [2024-03-13 10:48:31.083035]: Generating output signature exposures. +#> ✔ [2024-03-13 10:48:31.096095]: Done. +#> ℹ [2024-03-13 10:48:31.097506]: Calculating errors (Frobenius Norm). +#> ✔ [2024-03-13 10:48:31.11865]: Done. +#> ℹ [2024-03-13 10:48:31.120221]: 0.312 secs elapsed. +#> ℹ [2024-03-13 10:48:31.123379]: Getting bootstrap exposures (&errors/similarity) for different methods. +#> ℹ [2024-03-13 10:48:31.124774]: This step is time consuming, please be patient. +#> ℹ [2024-03-13 10:48:31.126741]: Processing sample `TCGA-AB-2802`. +#> ℹ [2024-03-13 10:48:32.395966]: Processing sample `TCGA-AB-2803`. +#> ℹ [2024-03-13 10:48:33.655948]: Processing sample `TCGA-AB-2804`. +#> ℹ [2024-03-13 10:48:34.960143]: Processing sample `TCGA-AB-2805`. +#> ℹ [2024-03-13 10:48:36.24868]: Processing sample `TCGA-AB-2806`. +#> ℹ [2024-03-13 10:48:37.570496]: Processing sample `TCGA-AB-2807`. +#> ℹ [2024-03-13 10:48:38.905095]: Processing sample `TCGA-AB-2808`. +#> ℹ [2024-03-13 10:48:40.251413]: Processing sample `TCGA-AB-2809`. +#> ℹ [2024-03-13 10:48:41.551707]: Processing sample `TCGA-AB-2810`. +#> ℹ [2024-03-13 10:48:42.919298]: Processing sample `TCGA-AB-2812`. +#> ℹ [2024-03-13 10:48:44.208806]: Processing sample `TCGA-AB-2813`. +#> ℹ [2024-03-13 10:48:45.543766]: Processing sample `TCGA-AB-2814`. +#> ℹ [2024-03-13 10:48:46.845868]: Processing sample `TCGA-AB-2816`. +#> ℹ [2024-03-13 10:48:48.192296]: Processing sample `TCGA-AB-2817`. +#> ℹ [2024-03-13 10:48:49.518848]: Processing sample `TCGA-AB-2818`. +#> ℹ [2024-03-13 10:48:50.860689]: Processing sample `TCGA-AB-2819`. +#> ℹ [2024-03-13 10:48:52.207212]: Processing sample `TCGA-AB-2820`. +#> ℹ [2024-03-13 10:48:53.545728]: Processing sample `TCGA-AB-2821`. +#> ℹ [2024-03-13 10:48:54.909579]: Processing sample `TCGA-AB-2822`. +#> ℹ [2024-03-13 10:48:56.259956]: Processing sample `TCGA-AB-2824`. +#> ℹ [2024-03-13 10:48:57.612445]: Processing sample `TCGA-AB-2826`. +#> ℹ [2024-03-13 10:48:58.956361]: Processing sample `TCGA-AB-2827`. +#> ℹ [2024-03-13 10:49:00.29764]: Processing sample `TCGA-AB-2828`. +#> ℹ [2024-03-13 10:49:01.651678]: Processing sample `TCGA-AB-2829`. +#> ℹ [2024-03-13 10:49:02.988061]: Processing sample `TCGA-AB-2830`. +#> ℹ [2024-03-13 10:49:04.348278]: Processing sample `TCGA-AB-2831`. +#> ℹ [2024-03-13 10:49:05.688132]: Processing sample `TCGA-AB-2832`. +#> ℹ [2024-03-13 10:49:07.018557]: Processing sample `TCGA-AB-2833`. +#> ℹ [2024-03-13 10:49:08.322914]: Processing sample `TCGA-AB-2835`. +#> ℹ [2024-03-13 10:49:09.655106]: Processing sample `TCGA-AB-2836`. +#> ℹ [2024-03-13 10:49:11.004648]: Processing sample `TCGA-AB-2838`. +#> ℹ [2024-03-13 10:49:12.3325]: Processing sample `TCGA-AB-2839`. +#> ℹ [2024-03-13 10:49:13.656049]: Processing sample `TCGA-AB-2841`. +#> ℹ [2024-03-13 10:49:14.975343]: Processing sample `TCGA-AB-2842`. +#> ℹ [2024-03-13 10:49:16.297359]: Processing sample `TCGA-AB-2843`. +#> ℹ [2024-03-13 10:49:17.647246]: Processing sample `TCGA-AB-2844`. +#> ℹ [2024-03-13 10:49:18.952904]: Processing sample `TCGA-AB-2845`. +#> ℹ [2024-03-13 10:49:20.298514]: Processing sample `TCGA-AB-2846`. +#> ℹ [2024-03-13 10:49:21.635396]: Processing sample `TCGA-AB-2847`. +#> ℹ [2024-03-13 10:49:22.975652]: Processing sample `TCGA-AB-2849`. +#> ℹ [2024-03-13 10:49:24.29361]: Processing sample `TCGA-AB-2850`. +#> ℹ [2024-03-13 10:49:25.617163]: Processing sample `TCGA-AB-2851`. +#> ℹ [2024-03-13 10:49:26.953113]: Processing sample `TCGA-AB-2853`. +#> ℹ [2024-03-13 10:49:28.31169]: Processing sample `TCGA-AB-2854`. +#> ℹ [2024-03-13 10:49:29.627376]: Processing sample `TCGA-AB-2855`. +#> ℹ [2024-03-13 10:49:30.985345]: Processing sample `TCGA-AB-2857`. +#> ℹ [2024-03-13 10:49:32.325152]: Processing sample `TCGA-AB-2858`. +#> ℹ [2024-03-13 10:49:33.63411]: Processing sample `TCGA-AB-2859`. +#> ℹ [2024-03-13 10:49:34.9546]: Processing sample `TCGA-AB-2860`. +#> ℹ [2024-03-13 10:49:36.240198]: Processing sample `TCGA-AB-2861`. +#> ℹ [2024-03-13 10:49:37.531909]: Processing sample `TCGA-AB-2862`. +#> ℹ [2024-03-13 10:49:38.813399]: Processing sample `TCGA-AB-2863`. +#> ℹ [2024-03-13 10:49:40.101139]: Processing sample `TCGA-AB-2864`. +#> ℹ [2024-03-13 10:49:41.383459]: Processing sample `TCGA-AB-2865`. +#> ℹ [2024-03-13 10:49:42.666143]: Processing sample `TCGA-AB-2867`. +#> ℹ [2024-03-13 10:49:43.960484]: Processing sample `TCGA-AB-2868`. +#> ℹ [2024-03-13 10:49:45.249294]: Processing sample `TCGA-AB-2869`. +#> ℹ [2024-03-13 10:49:46.520141]: Processing sample `TCGA-AB-2870`. +#> ℹ [2024-03-13 10:49:47.813735]: Processing sample `TCGA-AB-2871`. +#> ℹ [2024-03-13 10:49:49.120808]: Processing sample `TCGA-AB-2872`. +#> ℹ [2024-03-13 10:49:50.445767]: Processing sample `TCGA-AB-2874`. +#> ℹ [2024-03-13 10:49:51.754527]: Processing sample `TCGA-AB-2875`. +#> ℹ [2024-03-13 10:49:53.073076]: Processing sample `TCGA-AB-2876`. +#> ℹ [2024-03-13 10:49:54.373675]: Processing sample `TCGA-AB-2877`. +#> ℹ [2024-03-13 10:49:55.695214]: Processing sample `TCGA-AB-2878`. +#> ℹ [2024-03-13 10:49:56.99732]: Processing sample `TCGA-AB-2879`. +#> ℹ [2024-03-13 10:49:58.32365]: Processing sample `TCGA-AB-2881`. +#> ℹ [2024-03-13 10:49:59.647551]: Processing sample `TCGA-AB-2882`. +#> ℹ [2024-03-13 10:50:00.969243]: Processing sample `TCGA-AB-2884`. +#> ℹ [2024-03-13 10:50:02.291619]: Processing sample `TCGA-AB-2885`. +#> ℹ [2024-03-13 10:50:03.632535]: Processing sample `TCGA-AB-2886`. +#> ℹ [2024-03-13 10:50:04.949602]: Processing sample `TCGA-AB-2887`. +#> ℹ [2024-03-13 10:50:06.272891]: Processing sample `TCGA-AB-2888`. +#> ℹ [2024-03-13 10:50:07.59611]: Processing sample `TCGA-AB-2889`. +#> ℹ [2024-03-13 10:50:08.926262]: Processing sample `TCGA-AB-2890`. +#> ℹ [2024-03-13 10:50:10.275068]: Processing sample `TCGA-AB-2891`. +#> ℹ [2024-03-13 10:50:11.590017]: Processing sample `TCGA-AB-2894`. +#> ℹ [2024-03-13 10:50:12.945213]: Processing sample `TCGA-AB-2895`. +#> ℹ [2024-03-13 10:50:14.276197]: Processing sample `TCGA-AB-2897`. +#> ℹ [2024-03-13 10:50:15.60492]: Processing sample `TCGA-AB-2898`. +#> ℹ [2024-03-13 10:50:16.919326]: Processing sample `TCGA-AB-2899`. +#> ℹ [2024-03-13 10:50:18.259379]: Processing sample `TCGA-AB-2900`. +#> ℹ [2024-03-13 10:50:19.577184]: Processing sample `TCGA-AB-2901`. +#> ℹ [2024-03-13 10:50:20.917572]: Processing sample `TCGA-AB-2904`. +#> ℹ [2024-03-13 10:50:22.231785]: Processing sample `TCGA-AB-2905`. +#> ℹ [2024-03-13 10:50:23.552033]: Processing sample `TCGA-AB-2906`. +#> ℹ [2024-03-13 10:50:24.866477]: Processing sample `TCGA-AB-2907`. +#> ℹ [2024-03-13 10:50:26.192244]: Processing sample `TCGA-AB-2908`. +#> ℹ [2024-03-13 10:50:27.534319]: Processing sample `TCGA-AB-2910`. +#> ℹ [2024-03-13 10:50:28.846952]: Processing sample `TCGA-AB-2911`. +#> ℹ [2024-03-13 10:50:30.17773]: Processing sample `TCGA-AB-2912`. +#> ℹ [2024-03-13 10:50:31.521202]: Processing sample `TCGA-AB-2913`. +#> ℹ [2024-03-13 10:50:32.834384]: Processing sample `TCGA-AB-2914`. +#> ℹ [2024-03-13 10:50:34.165487]: Processing sample `TCGA-AB-2915`. +#> ℹ [2024-03-13 10:50:35.524467]: Processing sample `TCGA-AB-2916`. +#> ℹ [2024-03-13 10:50:36.838635]: Processing sample `TCGA-AB-2917`. +#> ℹ [2024-03-13 10:50:38.18873]: Processing sample `TCGA-AB-2919`. +#> ℹ [2024-03-13 10:50:39.502985]: Processing sample `TCGA-AB-2920`. +#> ℹ [2024-03-13 10:50:40.848347]: Processing sample `TCGA-AB-2921`. +#> ℹ [2024-03-13 10:50:42.192813]: Processing sample `TCGA-AB-2922`. +#> ℹ [2024-03-13 10:50:43.540581]: Processing sample `TCGA-AB-2923`. +#> ℹ [2024-03-13 10:50:44.88919]: Processing sample `TCGA-AB-2924`. +#> ℹ [2024-03-13 10:50:46.227546]: Processing sample `TCGA-AB-2925`. +#> ℹ [2024-03-13 10:50:47.540703]: Processing sample `TCGA-AB-2926`. +#> ℹ [2024-03-13 10:50:48.909526]: Processing sample `TCGA-AB-2927`. +#> ℹ [2024-03-13 10:50:50.229566]: Processing sample `TCGA-AB-2928`. +#> ℹ [2024-03-13 10:50:51.587188]: Processing sample `TCGA-AB-2929`. +#> ℹ [2024-03-13 10:50:52.950285]: Processing sample `TCGA-AB-2930`. +#> ℹ [2024-03-13 10:50:54.333439]: Processing sample `TCGA-AB-2931`. +#> ℹ [2024-03-13 10:50:55.656429]: Processing sample `TCGA-AB-2932`. +#> ℹ [2024-03-13 10:50:56.99632]: Processing sample `TCGA-AB-2934`. +#> ℹ [2024-03-13 10:50:58.329051]: Processing sample `TCGA-AB-2935`. +#> ℹ [2024-03-13 10:50:59.678164]: Processing sample `TCGA-AB-2936`. +#> ℹ [2024-03-13 10:51:01.012378]: Processing sample `TCGA-AB-2937`. +#> ℹ [2024-03-13 10:51:02.305403]: Processing sample `TCGA-AB-2938`. +#> ℹ [2024-03-13 10:51:03.582466]: Processing sample `TCGA-AB-2939`. +#> ℹ [2024-03-13 10:51:04.855023]: Processing sample `TCGA-AB-2940`. +#> ℹ [2024-03-13 10:51:06.127497]: Processing sample `TCGA-AB-2941`. +#> ℹ [2024-03-13 10:51:07.401881]: Processing sample `TCGA-AB-2943`. +#> ℹ [2024-03-13 10:51:08.663834]: Processing sample `TCGA-AB-2945`. +#> ℹ [2024-03-13 10:51:09.952823]: Processing sample `TCGA-AB-2946`. +#> ℹ [2024-03-13 10:51:11.31013]: Processing sample `TCGA-AB-2947`. +#> ℹ [2024-03-13 10:51:12.602024]: Processing sample `TCGA-AB-2949`. +#> ℹ [2024-03-13 10:51:13.885957]: Processing sample `TCGA-AB-2950`. +#> ℹ [2024-03-13 10:51:15.168115]: Processing sample `TCGA-AB-2952`. +#> ℹ [2024-03-13 10:51:16.45251]: Processing sample `TCGA-AB-2955`. +#> ℹ [2024-03-13 10:51:17.739712]: Processing sample `TCGA-AB-2956`. +#> ℹ [2024-03-13 10:51:19.080796]: Processing sample `TCGA-AB-2957`. +#> ℹ [2024-03-13 10:51:20.410381]: Processing sample `TCGA-AB-2959`. +#> ℹ [2024-03-13 10:51:21.730083]: Processing sample `TCGA-AB-2963`. +#> ℹ [2024-03-13 10:51:23.09314]: Processing sample `TCGA-AB-2964`. +#> ℹ [2024-03-13 10:51:24.40825]: Processing sample `TCGA-AB-2965`. +#> ℹ [2024-03-13 10:51:25.764359]: Processing sample `TCGA-AB-2966`. +#> ℹ [2024-03-13 10:51:27.083341]: Processing sample `TCGA-AB-2967`. +#> ℹ [2024-03-13 10:51:28.426753]: Processing sample `TCGA-AB-2968`. +#> ℹ [2024-03-13 10:51:29.754459]: Processing sample `TCGA-AB-2970`. +#> ℹ [2024-03-13 10:51:31.136456]: Processing sample `TCGA-AB-2971`. +#> ℹ [2024-03-13 10:51:32.510793]: Processing sample `TCGA-AB-2972`. +#> ℹ [2024-03-13 10:51:33.820951]: Processing sample `TCGA-AB-2973`. +#> ℹ [2024-03-13 10:51:35.239862]: Processing sample `TCGA-AB-2974`. +#> ℹ [2024-03-13 10:51:36.56035]: Processing sample `TCGA-AB-2975`. +#> ℹ [2024-03-13 10:51:37.910085]: Processing sample `TCGA-AB-2976`. +#> ℹ [2024-03-13 10:51:39.269342]: Processing sample `TCGA-AB-2977`. +#> ℹ [2024-03-13 10:51:40.621294]: Processing sample `TCGA-AB-2978`. +#> ℹ [2024-03-13 10:51:41.968635]: Processing sample `TCGA-AB-2979`. +#> ℹ [2024-03-13 10:51:43.303119]: Processing sample `TCGA-AB-2980`. +#> ℹ [2024-03-13 10:51:44.645596]: Processing sample `TCGA-AB-2981`. +#> ℹ [2024-03-13 10:51:46.020193]: Processing sample `TCGA-AB-2982`. +#> ℹ [2024-03-13 10:51:47.408903]: Processing sample `TCGA-AB-2983`. +#> ℹ [2024-03-13 10:51:48.777553]: Processing sample `TCGA-AB-2984`. +#> ℹ [2024-03-13 10:51:50.121754]: Processing sample `TCGA-AB-2985`. +#> ℹ [2024-03-13 10:51:51.491612]: Processing sample `TCGA-AB-2986`. +#> ℹ [2024-03-13 10:51:52.824721]: Processing sample `TCGA-AB-2987`. +#> ℹ [2024-03-13 10:51:54.23443]: Processing sample `TCGA-AB-2988`. +#> ℹ [2024-03-13 10:51:55.613137]: Processing sample `TCGA-AB-2989`. +#> ℹ [2024-03-13 10:51:57.012665]: Processing sample `TCGA-AB-2990`. +#> ℹ [2024-03-13 10:51:58.370311]: Processing sample `TCGA-AB-2991`. +#> ℹ [2024-03-13 10:51:59.712911]: Processing sample `TCGA-AB-2992`. +#> ℹ [2024-03-13 10:52:01.056572]: Processing sample `TCGA-AB-2993`. +#> ℹ [2024-03-13 10:52:02.406984]: Processing sample `TCGA-AB-2994`. +#> ℹ [2024-03-13 10:52:03.758658]: Processing sample `TCGA-AB-2995`. +#> ℹ [2024-03-13 10:52:05.114392]: Processing sample `TCGA-AB-2996`. +#> ℹ [2024-03-13 10:52:06.479587]: Processing sample `TCGA-AB-2997`. +#> ℹ [2024-03-13 10:52:07.820473]: Processing sample `TCGA-AB-2998`. +#> ℹ [2024-03-13 10:52:09.194096]: Processing sample `TCGA-AB-2999`. +#> ℹ [2024-03-13 10:52:10.56655]: Processing sample `TCGA-AB-3000`. +#> ℹ [2024-03-13 10:52:11.936671]: Processing sample `TCGA-AB-3001`. +#> ℹ [2024-03-13 10:52:13.30676]: Processing sample `TCGA-AB-3002`. +#> ℹ [2024-03-13 10:52:14.71273]: Processing sample `TCGA-AB-3005`. +#> ℹ [2024-03-13 10:52:16.082228]: Processing sample `TCGA-AB-3006`. +#> ℹ [2024-03-13 10:52:17.428633]: Processing sample `TCGA-AB-3007`. +#> ℹ [2024-03-13 10:52:18.772044]: Processing sample `TCGA-AB-3008`. +#> ℹ [2024-03-13 10:52:20.103501]: Processing sample `TCGA-AB-3009`. +#> ℹ [2024-03-13 10:52:21.39808]: Processing sample `TCGA-AB-3011`. +#> ℹ [2024-03-13 10:52:22.734886]: Processing sample `TCGA-AB-3012`. +#> ✔ [2024-03-13 10:52:24.066003]: Gotten. +#> ℹ [2024-03-13 10:52:24.068522]: Reporting p values... +#> ℹ [2024-03-13 10:52:24.070143]: Started. +#> ✔ [2024-03-13 10:52:24.071572]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.073589]: Done. +#> ℹ [2024-03-13 10:52:24.075021]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.076482]: Started. +#> ✔ [2024-03-13 10:52:24.077833]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.079669]: Done. +#> ℹ [2024-03-13 10:52:24.081107]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.0825]: Started. +#> ✔ [2024-03-13 10:52:24.083872]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.085659]: Done. +#> ℹ [2024-03-13 10:52:24.087056]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.088469]: Started. +#> ✔ [2024-03-13 10:52:24.089807]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.091584]: Done. +#> ℹ [2024-03-13 10:52:24.092983]: 0.004 secs elapsed. +#> ℹ [2024-03-13 10:52:24.094372]: Started. +#> ✔ [2024-03-13 10:52:24.095768]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.09754]: Done. +#> ℹ [2024-03-13 10:52:24.098918]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.100373]: Started. +#> ✔ [2024-03-13 10:52:24.101721]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.103514]: Done. +#> ℹ [2024-03-13 10:52:24.104914]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.106293]: Started. +#> ✔ [2024-03-13 10:52:24.107666]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.109522]: Done. +#> ℹ [2024-03-13 10:52:24.110914]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.112346]: Started. +#> ✔ [2024-03-13 10:52:24.113693]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.115505]: Done. +#> ℹ [2024-03-13 10:52:24.116894]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.118277]: Started. +#> ✔ [2024-03-13 10:52:24.119656]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.121441]: Done. +#> ℹ [2024-03-13 10:52:24.122881]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.124327]: Started. +#> ✔ [2024-03-13 10:52:24.125723]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.127507]: Done. +#> ℹ [2024-03-13 10:52:24.128911]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.130324]: Started. +#> ✔ [2024-03-13 10:52:24.131693]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.133599]: Done. +#> ℹ [2024-03-13 10:52:24.135033]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.136584]: Started. +#> ✔ [2024-03-13 10:52:24.137978]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.140013]: Done. +#> ℹ [2024-03-13 10:52:24.141466]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.142918]: Started. +#> ✔ [2024-03-13 10:52:24.144405]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.146494]: Done. +#> ℹ [2024-03-13 10:52:24.148009]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.149504]: Started. +#> ✔ [2024-03-13 10:52:24.150925]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.153191]: Done. +#> ℹ [2024-03-13 10:52:24.15473]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.156264]: Started. +#> ✔ [2024-03-13 10:52:24.157695]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.15988]: Done. +#> ℹ [2024-03-13 10:52:24.161394]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.162893]: Started. +#> ✔ [2024-03-13 10:52:24.164367]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.166484]: Done. +#> ℹ [2024-03-13 10:52:24.168016]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.16953]: Started. +#> ✔ [2024-03-13 10:52:24.170973]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.173107]: Done. +#> ℹ [2024-03-13 10:52:24.174622]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.176227]: Started. +#> ✔ [2024-03-13 10:52:24.177664]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.179795]: Done. +#> ℹ [2024-03-13 10:52:24.181286]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.182771]: Started. +#> ✔ [2024-03-13 10:52:24.184317]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.186349]: Done. +#> ℹ [2024-03-13 10:52:24.187847]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.189322]: Started. +#> ✔ [2024-03-13 10:52:24.190715]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.192658]: Done. +#> ℹ [2024-03-13 10:52:24.194131]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.19565]: Started. +#> ✔ [2024-03-13 10:52:24.197147]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.199113]: Done. +#> ℹ [2024-03-13 10:52:24.200621]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.202091]: Started. +#> ✔ [2024-03-13 10:52:24.203558]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.20551]: Done. +#> ℹ [2024-03-13 10:52:24.206961]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.208453]: Started. +#> ✔ [2024-03-13 10:52:24.209838]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.211756]: Done. +#> ℹ [2024-03-13 10:52:24.21321]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.214649]: Started. +#> ✔ [2024-03-13 10:52:24.216051]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.217898]: Done. +#> ℹ [2024-03-13 10:52:24.219353]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.220781]: Started. +#> ✔ [2024-03-13 10:52:24.222159]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.22409]: Done. +#> ℹ [2024-03-13 10:52:24.225528]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.226961]: Started. +#> ✔ [2024-03-13 10:52:24.228372]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.230278]: Done. +#> ℹ [2024-03-13 10:52:24.231758]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.233204]: Started. +#> ✔ [2024-03-13 10:52:24.234585]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.236452]: Done. +#> ℹ [2024-03-13 10:52:24.237874]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.23932]: Started. +#> ✔ [2024-03-13 10:52:24.240678]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.242491]: Done. +#> ℹ [2024-03-13 10:52:24.243974]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.245397]: Started. +#> ✔ [2024-03-13 10:52:24.24676]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.24861]: Done. +#> ℹ [2024-03-13 10:52:24.250024]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.251461]: Started. +#> ✔ [2024-03-13 10:52:24.252816]: Batch mode enabled. +#> ! [2024-03-13 10:52:24.254488]: NA result detected from t.test, reporting proportion as p value. +#> ✔ [2024-03-13 10:52:24.256186]: Done. +#> ℹ [2024-03-13 10:52:24.257604]: 0.006 secs elapsed. +#> ℹ [2024-03-13 10:52:24.259014]: Started. +#> ✔ [2024-03-13 10:52:24.260414]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.262252]: Done. +#> ℹ [2024-03-13 10:52:24.263726]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.265167]: Started. +#> ✔ [2024-03-13 10:52:24.266529]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.268367]: Done. +#> ℹ [2024-03-13 10:52:24.26978]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.271192]: Started. +#> ✔ [2024-03-13 10:52:24.272781]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.274618]: Done. +#> ℹ [2024-03-13 10:52:24.276065]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.277484]: Started. +#> ✔ [2024-03-13 10:52:24.278882]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.280751]: Done. +#> ℹ [2024-03-13 10:52:24.282168]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.283602]: Started. +#> ✔ [2024-03-13 10:52:24.284966]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.286796]: Done. +#> ℹ [2024-03-13 10:52:24.288256]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.289659]: Started. +#> ✔ [2024-03-13 10:52:24.291005]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.292809]: Done. +#> ℹ [2024-03-13 10:52:24.294228]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.295659]: Started. +#> ✔ [2024-03-13 10:52:24.297007]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.298789]: Done. +#> ℹ [2024-03-13 10:52:24.30022]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.301619]: Started. +#> ✔ [2024-03-13 10:52:24.302959]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.304771]: Done. +#> ℹ [2024-03-13 10:52:24.306173]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.307608]: Started. +#> ✔ [2024-03-13 10:52:24.308947]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.310727]: Done. +#> ℹ [2024-03-13 10:52:24.312189]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.313582]: Started. +#> ✔ [2024-03-13 10:52:24.314932]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.316735]: Done. +#> ℹ [2024-03-13 10:52:24.318132]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.319538]: Started. +#> ✔ [2024-03-13 10:52:24.320888]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.322659]: Done. +#> ℹ [2024-03-13 10:52:24.324094]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.325474]: Started. +#> ✔ [2024-03-13 10:52:24.326812]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.328598]: Done. +#> ℹ [2024-03-13 10:52:24.32999]: 0.004 secs elapsed. +#> ℹ [2024-03-13 10:52:24.331399]: Started. +#> ✔ [2024-03-13 10:52:24.332745]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.334516]: Done. +#> ℹ [2024-03-13 10:52:24.335968]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.337357]: Started. +#> ✔ [2024-03-13 10:52:24.338693]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.340469]: Done. +#> ℹ [2024-03-13 10:52:24.341878]: 0.004 secs elapsed. +#> ℹ [2024-03-13 10:52:24.343294]: Started. +#> ✔ [2024-03-13 10:52:24.344637]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.346393]: Done. +#> ℹ [2024-03-13 10:52:24.34784]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.349231]: Started. +#> ✔ [2024-03-13 10:52:24.350568]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.352354]: Done. +#> ℹ [2024-03-13 10:52:24.353745]: 0.004 secs elapsed. +#> ℹ [2024-03-13 10:52:24.355136]: Started. +#> ✔ [2024-03-13 10:52:24.356501]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.358286]: Done. +#> ℹ [2024-03-13 10:52:24.359703]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.361084]: Started. +#> ✔ [2024-03-13 10:52:24.362437]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.364235]: Done. +#> ℹ [2024-03-13 10:52:24.365626]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.367015]: Started. +#> ✔ [2024-03-13 10:52:24.368388]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.370144]: Done. +#> ℹ [2024-03-13 10:52:24.371556]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.372943]: Started. +#> ✔ [2024-03-13 10:52:24.374311]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.376123]: Done. +#> ℹ [2024-03-13 10:52:24.37753]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.378913]: Started. +#> ✔ [2024-03-13 10:52:24.380275]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.382025]: Done. +#> ℹ [2024-03-13 10:52:24.383456]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.384853]: Started. +#> ✔ [2024-03-13 10:52:24.386197]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.387982]: Done. +#> ℹ [2024-03-13 10:52:24.389382]: 0.004 secs elapsed. +#> ℹ [2024-03-13 10:52:24.390774]: Started. +#> ✔ [2024-03-13 10:52:24.392142]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.393899]: Done. +#> ℹ [2024-03-13 10:52:24.395321]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.396715]: Started. +#> ✔ [2024-03-13 10:52:24.398071]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.399915]: Done. +#> ℹ [2024-03-13 10:52:24.401326]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.402722]: Started. +#> ✔ [2024-03-13 10:52:24.404124]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.405941]: Done. +#> ℹ [2024-03-13 10:52:24.407384]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.40881]: Started. +#> ✔ [2024-03-13 10:52:24.41019]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.412063]: Done. +#> ℹ [2024-03-13 10:52:24.413491]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.414921]: Started. +#> ✔ [2024-03-13 10:52:24.416318]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.418137]: Done. +#> ℹ [2024-03-13 10:52:24.419601]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.421027]: Started. +#> ✔ [2024-03-13 10:52:24.422403]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.42424]: Done. +#> ℹ [2024-03-13 10:52:24.425677]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.42709]: Started. +#> ✔ [2024-03-13 10:52:24.428477]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.43027]: Done. +#> ℹ [2024-03-13 10:52:24.43173]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.433137]: Started. +#> ✔ [2024-03-13 10:52:24.434514]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.436337]: Done. +#> ℹ [2024-03-13 10:52:24.437744]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.439139]: Started. +#> ✔ [2024-03-13 10:52:24.440514]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.442293]: Done. +#> ℹ [2024-03-13 10:52:24.443723]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.445126]: Started. +#> ✔ [2024-03-13 10:52:24.446477]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.448289]: Done. +#> ℹ [2024-03-13 10:52:24.449733]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.451117]: Started. +#> ✔ [2024-03-13 10:52:24.452513]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.454311]: Done. +#> ℹ [2024-03-13 10:52:24.455788]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.457185]: Started. +#> ✔ [2024-03-13 10:52:24.458553]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.460406]: Done. +#> ℹ [2024-03-13 10:52:24.461944]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.463386]: Started. +#> ✔ [2024-03-13 10:52:24.464754]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.466567]: Done. +#> ℹ [2024-03-13 10:52:24.468032]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.469439]: Started. +#> ✔ [2024-03-13 10:52:24.470802]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.472632]: Done. +#> ℹ [2024-03-13 10:52:24.474061]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.475533]: Started. +#> ✔ [2024-03-13 10:52:24.476918]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.478742]: Done. +#> ℹ [2024-03-13 10:52:24.480211]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.48162]: Started. +#> ✔ [2024-03-13 10:52:24.482991]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.484819]: Done. +#> ℹ [2024-03-13 10:52:24.48624]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.487669]: Started. +#> ✔ [2024-03-13 10:52:24.489043]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.490848]: Done. +#> ℹ [2024-03-13 10:52:24.492331]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.493804]: Started. +#> ✔ [2024-03-13 10:52:24.495212]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.497116]: Done. +#> ℹ [2024-03-13 10:52:24.498628]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.500102]: Started. +#> ✔ [2024-03-13 10:52:24.501496]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.503384]: Done. +#> ℹ [2024-03-13 10:52:24.504884]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.506355]: Started. +#> ✔ [2024-03-13 10:52:24.507801]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.509821]: Done. +#> ℹ [2024-03-13 10:52:24.511355]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.512889]: Started. +#> ✔ [2024-03-13 10:52:24.514343]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.516327]: Done. +#> ℹ [2024-03-13 10:52:24.517813]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.519323]: Started. +#> ✔ [2024-03-13 10:52:24.520728]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.522575]: Done. +#> ℹ [2024-03-13 10:52:24.524059]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.525518]: Started. +#> ✔ [2024-03-13 10:52:24.526898]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.528949]: Done. +#> ℹ [2024-03-13 10:52:24.530522]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.532071]: Started. +#> ✔ [2024-03-13 10:52:24.533514]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.535482]: Done. +#> ℹ [2024-03-13 10:52:24.537068]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.538592]: Started. +#> ✔ [2024-03-13 10:52:24.540085]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.542005]: Done. +#> ℹ [2024-03-13 10:52:24.543515]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.545049]: Started. +#> ✔ [2024-03-13 10:52:24.546534]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.548522]: Done. +#> ℹ [2024-03-13 10:52:24.550073]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.551639]: Started. +#> ✔ [2024-03-13 10:52:24.553114]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.555072]: Done. +#> ℹ [2024-03-13 10:52:24.556648]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.558225]: Started. +#> ✔ [2024-03-13 10:52:24.559855]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.561945]: Done. +#> ℹ [2024-03-13 10:52:24.563565]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.56512]: Started. +#> ✔ [2024-03-13 10:52:24.566552]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.568522]: Done. +#> ℹ [2024-03-13 10:52:24.57]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.571549]: Started. +#> ✔ [2024-03-13 10:52:24.573017]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.574976]: Done. +#> ℹ [2024-03-13 10:52:24.576576]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.578119]: Started. +#> ✔ [2024-03-13 10:52:24.579539]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.581441]: Done. +#> ℹ [2024-03-13 10:52:24.583074]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.584799]: Started. +#> ✔ [2024-03-13 10:52:24.586403]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.588614]: Done. +#> ℹ [2024-03-13 10:52:24.590491]: 0.006 secs elapsed. +#> ℹ [2024-03-13 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10:52:24.625804]: Started. +#> ✔ [2024-03-13 10:52:24.627343]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.629329]: Done. +#> ℹ [2024-03-13 10:52:24.630849]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.632409]: Started. +#> ✔ [2024-03-13 10:52:24.633855]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.635802]: Done. +#> ℹ [2024-03-13 10:52:24.637285]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.638788]: Started. +#> ✔ [2024-03-13 10:52:24.640261]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.642143]: Done. +#> ℹ [2024-03-13 10:52:24.643649]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.645135]: Started. +#> ✔ [2024-03-13 10:52:24.646563]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.648473]: Done. +#> ℹ [2024-03-13 10:52:24.649935]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.651399]: Started. +#> ✔ [2024-03-13 10:52:24.652797]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.654756]: Done. +#> ℹ [2024-03-13 10:52:24.65624]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.657684]: Started. +#> ✔ [2024-03-13 10:52:24.659091]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.660965]: Done. +#> ℹ [2024-03-13 10:52:24.662418]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.663885]: Started. +#> ✔ [2024-03-13 10:52:24.665303]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.667132]: Done. +#> ℹ [2024-03-13 10:52:24.668614]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.670068]: Started. +#> ✔ [2024-03-13 10:52:24.671512]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.673356]: Done. +#> ℹ [2024-03-13 10:52:24.674818]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.676284]: Started. +#> ✔ [2024-03-13 10:52:24.677675]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.67954]: Done. +#> ℹ [2024-03-13 10:52:24.680991]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.682429]: Started. +#> ✔ [2024-03-13 10:52:24.683843]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.6857]: Done. +#> ℹ [2024-03-13 10:52:24.687146]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.688628]: Started. +#> ✔ [2024-03-13 10:52:24.690015]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.69188]: Done. +#> ℹ [2024-03-13 10:52:24.693348]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.694806]: Started. +#> ✔ [2024-03-13 10:52:24.696245]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.698162]: Done. +#> ℹ [2024-03-13 10:52:24.69966]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.701125]: Started. +#> ✔ [2024-03-13 10:52:24.702543]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.704417]: Done. +#> ℹ [2024-03-13 10:52:24.705857]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.70731]: Started. +#> ✔ [2024-03-13 10:52:24.708711]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.710524]: Done. +#> ℹ [2024-03-13 10:52:24.71198]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.713412]: Started. +#> ✔ [2024-03-13 10:52:24.714805]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.716653]: Done. +#> ℹ [2024-03-13 10:52:24.718109]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.719567]: Started. +#> ✔ [2024-03-13 10:52:24.720965]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.722788]: Done. +#> ℹ [2024-03-13 10:52:24.724265]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.725697]: Started. +#> ✔ [2024-03-13 10:52:24.727101]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.728993]: Done. +#> ℹ [2024-03-13 10:52:24.730444]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.731916]: Started. +#> ✔ [2024-03-13 10:52:24.733329]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.735186]: Done. +#> ℹ [2024-03-13 10:52:24.73666]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.738108]: Started. +#> ✔ [2024-03-13 10:52:24.739529]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.741374]: Done. +#> ℹ [2024-03-13 10:52:24.742849]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.744398]: Started. +#> ✔ [2024-03-13 10:52:24.745825]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.747693]: Done. +#> ℹ [2024-03-13 10:52:24.749169]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.750611]: Started. +#> ✔ [2024-03-13 10:52:24.752031]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.753859]: Done. +#> ℹ [2024-03-13 10:52:24.755354]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.756804]: Started. +#> ✔ [2024-03-13 10:52:24.758199]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.760103]: Done. +#> ℹ [2024-03-13 10:52:24.761565]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.763]: Started. +#> ✔ [2024-03-13 10:52:24.764424]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.766266]: Done. +#> ℹ [2024-03-13 10:52:24.767741]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.769192]: Started. +#> ✔ [2024-03-13 10:52:24.770587]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.772433]: Done. +#> ℹ [2024-03-13 10:52:24.773889]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.775367]: Started. +#> ✔ [2024-03-13 10:52:24.776776]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.778619]: Done. +#> ℹ [2024-03-13 10:52:24.780128]: 0.005 secs elapsed. +#> ℹ [2024-03-13 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10:52:24.812721]: Started. +#> ✔ [2024-03-13 10:52:24.814119]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.815989]: Done. +#> ℹ [2024-03-13 10:52:24.817433]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.818866]: Started. +#> ✔ [2024-03-13 10:52:24.820296]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.822106]: Done. +#> ℹ [2024-03-13 10:52:24.823564]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.825009]: Started. +#> ✔ [2024-03-13 10:52:24.826403]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.828236]: Done. +#> ℹ [2024-03-13 10:52:24.829672]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.831101]: Started. +#> ✔ [2024-03-13 10:52:24.832505]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.834323]: Done. +#> ℹ [2024-03-13 10:52:24.835789]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.837218]: Started. +#> ✔ [2024-03-13 10:52:24.8386]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.841255]: Done. +#> ℹ [2024-03-13 10:52:24.843414]: 0.006 secs elapsed. +#> ℹ [2024-03-13 10:52:24.845536]: Started. +#> ✔ [2024-03-13 10:52:24.847622]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.850266]: Done. +#> ℹ [2024-03-13 10:52:24.852441]: 0.007 secs elapsed. +#> ℹ [2024-03-13 10:52:24.854578]: Started. +#> ✔ [2024-03-13 10:52:24.856676]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.859357]: Done. +#> ℹ [2024-03-13 10:52:24.861476]: 0.007 secs elapsed. +#> ℹ [2024-03-13 10:52:24.863653]: Started. +#> ✔ [2024-03-13 10:52:24.865835]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.86849]: Done. +#> ℹ [2024-03-13 10:52:24.870212]: 0.007 secs elapsed. +#> ℹ [2024-03-13 10:52:24.8717]: Started. +#> ✔ [2024-03-13 10:52:24.873113]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.874949]: Done. +#> ℹ [2024-03-13 10:52:24.876519]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.87796]: Started. +#> ✔ [2024-03-13 10:52:24.879484]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.881329]: Done. +#> ℹ [2024-03-13 10:52:24.882773]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.884313]: Started. +#> ✔ [2024-03-13 10:52:24.88571]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.887597]: Done. +#> ℹ [2024-03-13 10:52:24.889072]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.890544]: Started. +#> ✔ [2024-03-13 10:52:24.891958]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.893824]: Done. +#> ℹ [2024-03-13 10:52:24.8953]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.896768]: Started. +#> ✔ [2024-03-13 10:52:24.898154]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.900016]: Done. +#> ℹ [2024-03-13 10:52:24.901456]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.902901]: Started. +#> ✔ [2024-03-13 10:52:24.904346]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.906193]: Done. +#> ℹ [2024-03-13 10:52:24.907656]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.909104]: Started. +#> ✔ [2024-03-13 10:52:24.910518]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.912367]: Done. +#> ℹ [2024-03-13 10:52:24.913806]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.915299]: Started. +#> ✔ [2024-03-13 10:52:24.916721]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.918549]: Done. +#> ℹ [2024-03-13 10:52:24.920051]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.921496]: Started. +#> ✔ [2024-03-13 10:52:24.922904]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.924747]: Done. +#> ℹ [2024-03-13 10:52:24.92618]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.927657]: Started. +#> ✔ [2024-03-13 10:52:24.929061]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.930868]: Done. +#> ℹ [2024-03-13 10:52:24.932343]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.933786]: Started. +#> ✔ [2024-03-13 10:52:24.935213]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.937085]: Done. +#> ℹ [2024-03-13 10:52:24.938528]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:52:24.939977]: Started. +#> ✔ [2024-03-13 10:52:24.941388]: Batch mode enabled. +#> ✔ [2024-03-13 10:52:24.94319]: Done. +#> ℹ [2024-03-13 10:52:24.944697]: 0.005 secs elapsed. +#> ℹ [2024-03-13 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10:52:27.135447]: Started. +#> ℹ [2024-03-13 10:52:27.15441]: Plotting. +#> ℹ [2024-03-13 10:52:27.200206]: 0.065 secs elapsed. #> Warning: Removed 21 rows containing non-finite outside the scale range #> (`stat_boxplot()`). #> Warning: Removed 21 rows containing missing values or values outside the scale range diff --git a/reference/sig_auto_extract.html b/reference/sig_auto_extract.html index e2743410..3ec4fffb 100644 --- a/reference/sig_auto_extract.html +++ b/reference/sig_auto_extract.html @@ -226,34 +226,34 @@

Examples

#> -Summarizing #> -Processing clinical data #> --Missing clinical data -#> -Finished in 0.159s elapsed (0.201s cpu) +#> -Finished in 0.170s elapsed (0.211s cpu) mt_tally <- sig_tally( laml, ref_genome = "BSgenome.Hsapiens.UCSC.hg19", use_syn = TRUE ) -#> ℹ [2024-03-08 02:37:17.043402]: Started. -#> ℹ [2024-03-08 02:37:17.047416]: We would assume you marked all variants' position in + strand. -#> ✔ [2024-03-08 02:37:17.049053]: Reference genome loaded. -#> ✔ [2024-03-08 02:37:17.053121]: Variants from MAF object queried. -#> ✔ [2024-03-08 02:37:17.055398]: Chromosome names checked. -#> ✔ [2024-03-08 02:37:17.058443]: Sex chromosomes properly handled. -#> ✔ [2024-03-08 02:37:17.060012]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. -#> ✔ [2024-03-08 02:37:17.06488]: Variant start and end position checked. -#> ✔ [2024-03-08 02:37:17.068601]: Variant data for matrix generation preprocessed. -#> ℹ [2024-03-08 02:37:17.069931]: SBS matrix generation - start. -#> ℹ [2024-03-08 02:37:17.071712]: Extracting 5' and 3' adjacent bases. -#> ℹ [2024-03-08 02:37:17.346889]: Extracting +/- 20bp around mutated bases for background C>T estimation. -#> ℹ [2024-03-08 02:37:17.678005]: Estimating APOBEC enrichment scores. -#> ℹ [2024-03-08 02:37:17.679862]: Performing one-way Fisher's test for APOBEC enrichment. -#> ✔ [2024-03-08 02:37:17.752696]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) -#> ℹ [2024-03-08 02:37:17.756081]: Creating SBS sample-by-component matrices. -#> ✔ [2024-03-08 02:37:17.760361]: SBS-6 matrix created. -#> ✔ [2024-03-08 02:37:17.765128]: SBS-96 matrix created. -#> ✔ [2024-03-08 02:37:17.778998]: SBS-1536 matrix created. -#> ℹ [2024-03-08 02:37:17.780383]: Return SBS-96 as major matrix. -#> ✔ [2024-03-08 02:37:17.782782]: Done. -#> ℹ [2024-03-08 02:37:17.784163]: 0.741 secs elapsed. +#> ℹ [2024-03-13 10:52:39.321204]: Started. +#> ℹ [2024-03-13 10:52:39.325443]: We would assume you marked all variants' position in + strand. +#> ✔ [2024-03-13 10:52:39.327311]: Reference genome loaded. +#> ✔ [2024-03-13 10:52:39.33178]: Variants from MAF object queried. +#> ✔ [2024-03-13 10:52:39.334143]: Chromosome names checked. +#> ✔ [2024-03-13 10:52:39.337384]: Sex chromosomes properly handled. +#> ✔ [2024-03-13 10:52:39.339015]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. +#> ✔ [2024-03-13 10:52:39.344189]: Variant start and end position checked. +#> ✔ [2024-03-13 10:52:39.348312]: Variant data for matrix generation preprocessed. +#> ℹ [2024-03-13 10:52:39.349706]: SBS matrix generation - start. +#> ℹ [2024-03-13 10:52:39.351612]: Extracting 5' and 3' adjacent bases. +#> ℹ [2024-03-13 10:52:39.666478]: Extracting +/- 20bp around mutated bases for background C>T estimation. +#> ℹ [2024-03-13 10:52:40.014906]: Estimating APOBEC enrichment scores. +#> ℹ [2024-03-13 10:52:40.016941]: Performing one-way Fisher's test for APOBEC enrichment. +#> ✔ [2024-03-13 10:52:40.091566]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) +#> ℹ [2024-03-13 10:52:40.095167]: Creating SBS sample-by-component matrices. +#> ✔ [2024-03-13 10:52:40.099787]: SBS-6 matrix created. +#> ✔ [2024-03-13 10:52:40.104901]: SBS-96 matrix created. +#> ✔ [2024-03-13 10:52:40.119379]: SBS-1536 matrix created. +#> ℹ [2024-03-13 10:52:40.121194]: Return SBS-96 as major matrix. +#> ✔ [2024-03-13 10:52:40.124294]: Done. +#> ℹ [2024-03-13 10:52:40.125776]: 0.805 secs elapsed. x <- sig_auto_extract(mt_tally$nmf_matrix, strategy = "ms", nrun = 3, ref_sigs = "legacy" @@ -716,9 +716,9 @@

Examples

#> # A tibble: 3 × 5 #> Run K posterior file similarity_to_ref #> <int> <int> <dbl> <chr> <dbl> -#> 1 2 2 9714. /tmp/RtmpXZeTRm/BayesNMF.2.rds 0.718 -#> 2 3 2 9711. /tmp/RtmpXZeTRm/BayesNMF.3.rds 0.676 -#> 3 1 3 9676. /tmp/RtmpXZeTRm/BayesNMF.1.rds 0.611 +#> 1 2 2 9714. /tmp/RtmpT86DiN/BayesNMF.2.rds 0.718 +#> 2 3 2 9711. /tmp/RtmpT86DiN/BayesNMF.3.rds 0.676 +#> 3 1 3 9676. /tmp/RtmpT86DiN/BayesNMF.1.rds 0.611 #> #> $Raw$W #> Sig1 Sig2 diff --git a/reference/sig_estimate.html b/reference/sig_estimate.html index 2718de3f..c0e136f4 100644 --- a/reference/sig_estimate.html +++ b/reference/sig_estimate.html @@ -315,10 +315,10 @@

Examples

#> 4 brunet random 1 KL 4 0.9084143 0.7776175 876.3489 #> 5 brunet random 1 KL 5 0.9089332 0.8287342 753.5275 #> evar silhouette.coef silhouette.basis residuals niter cpu cpu.all nrun -#> 2 0.9968140 1.0000000 1.0000000 289.6950 440 0.024 7.108 5 -#> 3 0.9985107 0.7821464 0.7463076 222.6087 770 0.042 6.558 5 -#> 4 0.9989960 0.7206650 0.6606767 174.0583 600 0.034 6.590 5 -#> 5 0.9991367 0.4363604 0.7187290 126.1886 960 0.052 6.588 5 +#> 2 0.9968140 1.0000000 1.0000000 289.6950 440 0.024 7.264 5 +#> 3 0.9985107 0.7821464 0.7463076 222.6087 770 0.041 7.325 5 +#> 4 0.9989960 0.7206650 0.6606767 174.0583 600 0.038 7.479 5 +#> 5 0.9991367 0.4363604 0.7187290 126.1886 960 0.055 7.372 5 #> cophenetic dispersion silhouette.consensus #> 2 0.9961624 0.8848 0.9550000 #> 3 0.8995319 0.5456 0.5973343 @@ -352,10 +352,10 @@

Examples

#> 4 brunet random 1 KL 4 0.9084143 0.7776175 876.3489 #> 5 brunet random 1 KL 5 0.9089332 0.8287342 753.5275 #> evar silhouette.coef silhouette.basis residuals niter cpu cpu.all nrun -#> 2 0.9968140 1.0000000 1.0000000 289.6950 440 0.024 7.108 5 -#> 3 0.9985107 0.7821464 0.7463076 222.6087 770 0.042 6.558 5 -#> 4 0.9989960 0.7206650 0.6606767 174.0583 600 0.034 6.590 5 -#> 5 0.9991367 0.4363604 0.7187290 126.1886 960 0.052 6.588 5 +#> 2 0.9968140 1.0000000 1.0000000 289.6950 440 0.024 7.264 5 +#> 3 0.9985107 0.7821464 0.7463076 222.6087 770 0.041 7.325 5 +#> 4 0.9989960 0.7206650 0.6606767 174.0583 600 0.038 7.479 5 +#> 5 0.9991367 0.4363604 0.7187290 126.1886 960 0.055 7.372 5 #> cophenetic dispersion silhouette.consensus #> 2 0.9961624 0.8848 0.9550000 #> 3 0.8995319 0.5456 0.5973343 diff --git a/reference/sig_fit.html b/reference/sig_fit.html index 51005805..f95a43b5 100644 --- a/reference/sig_fit.html +++ b/reference/sig_fit.html @@ -254,93 +254,93 @@

Examples

z <- get_groups(H_dt_rel, method = "k-means") show_groups(z) } -#> ℹ [2024-03-08 02:38:08.21295]: Started. -#> ℹ [2024-03-08 02:38:08.214621]: Signature index not detected. -#> ✔ [2024-03-08 02:38:08.216022]: Signature matrix/data.frame detected. -#> ✔ [2024-03-08 02:38:08.217362]: Database and index checked. -#> ✔ [2024-03-08 02:38:08.218759]: Signature normalized. -#> ℹ [2024-03-08 02:38:08.220111]: Checking row number for catalog matrix and signature matrix. -#> ✔ [2024-03-08 02:38:08.221435]: Checked. -#> ✔ [2024-03-08 02:38:08.222758]: Method 'QP' detected. -#> ✔ [2024-03-08 02:38:08.224077]: Corresponding function generated. -#> ℹ [2024-03-08 02:38:08.225367]: Calling function. -#> ℹ [2024-03-08 02:38:08.226862]: Fitting sample: samp1 -#> ℹ [2024-03-08 02:38:08.228331]: Fitting sample: samp2 -#> ℹ [2024-03-08 02:38:08.229728]: Fitting sample: samp3 -#> ℹ [2024-03-08 02:38:08.231134]: Fitting sample: samp4 -#> ✔ [2024-03-08 02:38:08.232533]: Done. -#> ℹ [2024-03-08 02:38:08.233856]: Generating output signature exposures. -#> ✔ [2024-03-08 02:38:08.235687]: Done. -#> ℹ [2024-03-08 02:38:08.237083]: 0.024 secs elapsed. -#> ℹ [2024-03-08 02:38:08.238495]: Started. -#> ℹ [2024-03-08 02:38:08.239832]: Signature index not detected. -#> ✔ [2024-03-08 02:38:08.241161]: Signature matrix/data.frame detected. -#> ✔ [2024-03-08 02:38:08.242488]: Database and index checked. -#> ✔ [2024-03-08 02:38:08.243911]: Signature normalized. -#> ℹ [2024-03-08 02:38:08.245237]: Checking row number for catalog matrix and signature matrix. -#> ✔ [2024-03-08 02:38:08.246565]: Checked. -#> ✔ [2024-03-08 02:38:08.24791]: Method 'QP' detected. -#> ✔ [2024-03-08 02:38:08.249227]: Corresponding function generated. -#> ℹ [2024-03-08 02:38:08.250532]: Calling function. -#> ℹ [2024-03-08 02:38:08.251995]: Fitting sample: samp1 -#> ✔ [2024-03-08 02:38:08.253401]: The cosine similarity is very high, just return result. -#> ℹ [2024-03-08 02:38:08.254745]: Fitting sample: samp2 -#> ✔ [2024-03-08 02:38:08.256153]: The cosine similarity is very high, just return result. -#> ℹ [2024-03-08 02:38:08.25748]: Fitting sample: samp3 -#> ✔ [2024-03-08 02:38:08.258888]: The cosine similarity is very high, just return result. -#> ℹ [2024-03-08 02:38:08.260218]: Fitting sample: samp4 -#> ✔ [2024-03-08 02:38:08.261606]: The cosine similarity is very high, just return result. -#> ✔ [2024-03-08 02:38:08.262969]: Done. -#> ℹ [2024-03-08 02:38:08.264287]: Generating output signature exposures. -#> ✔ [2024-03-08 02:38:08.274283]: Done. -#> ℹ [2024-03-08 02:38:08.275729]: 0.037 secs elapsed. -#> ℹ [2024-03-08 02:38:08.277399]: Started. -#> ℹ [2024-03-08 02:38:08.278759]: Checking input format. -#> ✔ [2024-03-08 02:38:08.287648]: Checked. -#> ℹ [2024-03-08 02:38:08.289073]: Checking filters. -#> ℹ [2024-03-08 02:38:08.290459]: Checked. -#> ℹ [2024-03-08 02:38:08.294527]: Plotting. -#> ℹ [2024-03-08 02:38:08.338103]: 0.061 secs elapsed. -#> ℹ [2024-03-08 02:38:08.339656]: Started. -#> ℹ [2024-03-08 02:38:08.340997]: Checking input format. -#> ✔ [2024-03-08 02:38:08.342367]: Checked. -#> ℹ [2024-03-08 02:38:08.343727]: Checking filters. -#> ℹ [2024-03-08 02:38:08.345072]: Checked. -#> ℹ [2024-03-08 02:38:08.349356]: Plotting. -#> ℹ [2024-03-08 02:38:08.392283]: 0.053 secs elapsed. -#> ℹ [2024-03-08 02:38:08.393794]: Started. -#> ℹ [2024-03-08 02:38:08.395164]: Signature index not detected. -#> ✔ [2024-03-08 02:38:08.396513]: Signature matrix/data.frame detected. -#> ✔ [2024-03-08 02:38:08.397868]: Database and index checked. -#> ✔ [2024-03-08 02:38:08.399306]: Signature normalized. -#> ℹ [2024-03-08 02:38:08.400627]: Checking row number for catalog matrix and signature matrix. -#> ✔ [2024-03-08 02:38:08.401944]: Checked. -#> ✔ [2024-03-08 02:38:08.403278]: Method 'QP' detected. -#> ✔ [2024-03-08 02:38:08.404588]: Corresponding function generated. -#> ℹ [2024-03-08 02:38:08.40589]: Calling function. -#> ℹ [2024-03-08 02:38:08.407374]: Fitting sample: samp1 -#> ℹ [2024-03-08 02:38:08.408824]: Fitting sample: samp2 -#> ℹ [2024-03-08 02:38:08.410205]: Fitting sample: samp3 -#> ℹ [2024-03-08 02:38:08.41161]: Fitting sample: samp4 -#> ✔ [2024-03-08 02:38:08.412993]: Done. -#> ℹ [2024-03-08 02:38:08.4143]: Generating output signature exposures. -#> ✔ [2024-03-08 02:38:08.424047]: Done. -#> ℹ [2024-03-08 02:38:08.425458]: 0.032 secs elapsed. -#> ℹ [2024-03-08 02:38:08.426868]: Started. -#> ✔ [2024-03-08 02:38:08.428193]: A 'data.table' detected. -#> ✔ [2024-03-08 02:38:08.429515]: Method checked. -#> ✔ [2024-03-08 02:38:08.430956]: Exposure should be relative checked. -#> ℹ [2024-03-08 02:38:08.432436]: Running k-means with 2 clusters... -#> ℹ [2024-03-08 02:38:08.434302]: Generating a table of group and signature contribution (stored in 'map_table' attr): +#> ℹ [2024-03-13 10:53:39.49291]: Started. +#> ℹ [2024-03-13 10:53:39.494659]: Signature index not detected. +#> ✔ [2024-03-13 10:53:39.496121]: Signature matrix/data.frame detected. +#> ✔ [2024-03-13 10:53:39.497574]: Database and index checked. +#> ✔ [2024-03-13 10:53:39.499181]: Signature normalized. +#> ℹ [2024-03-13 10:53:39.500638]: Checking row number for catalog matrix and signature matrix. +#> ✔ [2024-03-13 10:53:39.502008]: Checked. +#> ✔ [2024-03-13 10:53:39.503396]: Method 'QP' detected. +#> ✔ [2024-03-13 10:53:39.50475]: Corresponding function generated. +#> ℹ [2024-03-13 10:53:39.506074]: Calling function. +#> ℹ [2024-03-13 10:53:39.507678]: Fitting sample: samp1 +#> ℹ [2024-03-13 10:53:39.509166]: Fitting sample: samp2 +#> ℹ [2024-03-13 10:53:39.510616]: Fitting sample: samp3 +#> ℹ [2024-03-13 10:53:39.512077]: Fitting sample: samp4 +#> ✔ [2024-03-13 10:53:39.51349]: Done. +#> ℹ [2024-03-13 10:53:39.514842]: Generating output signature exposures. +#> ✔ [2024-03-13 10:53:39.516775]: Done. +#> ℹ [2024-03-13 10:53:39.518198]: 0.025 secs elapsed. +#> ℹ [2024-03-13 10:53:39.519676]: Started. +#> ℹ [2024-03-13 10:53:39.521026]: Signature index not detected. +#> ✔ [2024-03-13 10:53:39.522402]: Signature matrix/data.frame detected. +#> ✔ [2024-03-13 10:53:39.523793]: Database and index checked. +#> ✔ [2024-03-13 10:53:39.525249]: Signature normalized. +#> ℹ [2024-03-13 10:53:39.526602]: Checking row number for catalog matrix and signature matrix. +#> ✔ [2024-03-13 10:53:39.527973]: Checked. +#> ✔ [2024-03-13 10:53:39.529308]: Method 'QP' detected. +#> ✔ [2024-03-13 10:53:39.530639]: Corresponding function generated. +#> ℹ [2024-03-13 10:53:39.532011]: Calling function. +#> ℹ [2024-03-13 10:53:39.533556]: Fitting sample: samp1 +#> ✔ [2024-03-13 10:53:39.535044]: The cosine similarity is very high, just return result. +#> ℹ [2024-03-13 10:53:39.536447]: Fitting sample: samp2 +#> ✔ [2024-03-13 10:53:39.537874]: The cosine similarity is very high, just return result. +#> ℹ [2024-03-13 10:53:39.53924]: Fitting sample: samp3 +#> ✔ [2024-03-13 10:53:39.540682]: The cosine similarity is very high, just return result. +#> ℹ [2024-03-13 10:53:39.542042]: Fitting sample: samp4 +#> ✔ [2024-03-13 10:53:39.543491]: The cosine similarity is very high, just return result. +#> ✔ [2024-03-13 10:53:39.544858]: Done. +#> ℹ [2024-03-13 10:53:39.546206]: Generating output signature exposures. +#> ✔ [2024-03-13 10:53:39.556133]: Done. +#> ℹ [2024-03-13 10:53:39.557641]: 0.038 secs elapsed. +#> ℹ [2024-03-13 10:53:39.559424]: Started. +#> ℹ [2024-03-13 10:53:39.560828]: Checking input format. +#> ✔ [2024-03-13 10:53:39.569675]: Checked. +#> ℹ [2024-03-13 10:53:39.57115]: Checking filters. +#> ℹ [2024-03-13 10:53:39.572593]: Checked. +#> ℹ [2024-03-13 10:53:39.576726]: Plotting. +#> ℹ [2024-03-13 10:53:39.623562]: 0.064 secs elapsed. +#> ℹ [2024-03-13 10:53:39.625447]: Started. +#> ℹ [2024-03-13 10:53:39.627068]: Checking input format. +#> ✔ [2024-03-13 10:53:39.628686]: Checked. +#> ℹ [2024-03-13 10:53:39.630128]: Checking filters. +#> ℹ [2024-03-13 10:53:39.631566]: Checked. +#> ℹ [2024-03-13 10:53:39.636372]: Plotting. +#> ℹ [2024-03-13 10:53:39.682562]: 0.057 secs elapsed. +#> ℹ [2024-03-13 10:53:39.68447]: Started. +#> ℹ [2024-03-13 10:53:39.68604]: Signature index not detected. +#> ✔ [2024-03-13 10:53:39.68758]: Signature matrix/data.frame detected. +#> ✔ [2024-03-13 10:53:39.689054]: Database and index checked. +#> ✔ [2024-03-13 10:53:39.69057]: Signature normalized. +#> ℹ [2024-03-13 10:53:39.691981]: Checking row number for catalog matrix and signature matrix. +#> ✔ [2024-03-13 10:53:39.693363]: Checked. +#> ✔ [2024-03-13 10:53:39.694733]: Method 'QP' detected. +#> ✔ [2024-03-13 10:53:39.696114]: Corresponding function generated. +#> ℹ [2024-03-13 10:53:39.69754]: Calling function. +#> ℹ [2024-03-13 10:53:39.69912]: Fitting sample: samp1 +#> ℹ [2024-03-13 10:53:39.700654]: Fitting sample: samp2 +#> ℹ [2024-03-13 10:53:39.7021]: Fitting sample: samp3 +#> ℹ [2024-03-13 10:53:39.703554]: Fitting sample: samp4 +#> ✔ [2024-03-13 10:53:39.704977]: Done. +#> ℹ [2024-03-13 10:53:39.706329]: Generating output signature exposures. +#> ✔ [2024-03-13 10:53:39.716386]: Done. +#> ℹ [2024-03-13 10:53:39.717954]: 0.033 secs elapsed. +#> ℹ [2024-03-13 10:53:39.719489]: Started. +#> ✔ [2024-03-13 10:53:39.720892]: A 'data.table' detected. +#> ✔ [2024-03-13 10:53:39.722264]: Method checked. +#> ✔ [2024-03-13 10:53:39.723783]: Exposure should be relative checked. +#> ℹ [2024-03-13 10:53:39.725341]: Running k-means with 2 clusters... +#> ℹ [2024-03-13 10:53:39.727329]: Generating a table of group and signature contribution (stored in 'map_table' attr): #> sig1 sig2 #> 1 0.31746 0.68254 #> 2 0.10000 0.90000 -#> ℹ [2024-03-08 02:38:08.435724]: Assigning a group to a signature with the maximum fraction... -#> ℹ [2024-03-08 02:38:08.439181]: Summarizing... +#> ℹ [2024-03-13 10:53:39.728767]: Assigning a group to a signature with the maximum fraction... +#> ℹ [2024-03-13 10:53:39.732564]: Summarizing... #> group #1: 3 samples with sig2 enriched. #> group #2: 1 samples with sig2 enriched. -#> ! [2024-03-08 02:38:08.440991]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary). -#> ℹ [2024-03-08 02:38:08.442359]: 0.015 secs elapsed. +#> ! [2024-03-13 10:53:39.734486]: The 'enrich_sig' column is set to dominant signature in one group, please check and make it consistent with biological meaning (correct it by hand if necessary). +#> ℹ [2024-03-13 10:53:39.735925]: 0.016 secs elapsed. # if (requireNamespace("GenSA", quietly = TRUE)) { diff --git a/reference/sig_fit_bootstrap.html b/reference/sig_fit_bootstrap.html index 14707fe5..c8da4b55 100644 --- a/reference/sig_fit_bootstrap.html +++ b/reference/sig_fit_bootstrap.html @@ -249,10 +249,10 @@

Examples

# find_suboptimal = TRUE # ) } -#> ℹ [2024-03-08 02:38:08.839464]: Started. -#> ℹ [2024-03-08 02:38:08.841134]: Checking catalog. -#> ✔ [2024-03-08 02:38:08.842508]: Done. -#> ℹ [2024-03-08 02:38:08.843906]: About to start bootstrap. +#> ℹ [2024-03-13 10:53:40.196531]: Started. +#> ℹ [2024-03-13 10:53:40.19839]: Checking catalog. +#> ✔ [2024-03-13 10:53:40.19986]: Done. +#> ℹ [2024-03-13 10:53:40.201288]: About to start bootstrap. #> → Bootstrapping 10 times. #> → Total 10 times, starting no.1. #> → Total 10 times, starting no.2. @@ -266,18 +266,18 @@

Examples

#> → Total 10 times, starting no.10. #> Bootstrap done. #> -#> ✔ [2024-03-08 02:38:09.143026]: Signature exposures collected. -#> ✔ [2024-03-08 02:38:09.144432]: Errors and similarity collected. -#> ✔ [2024-03-08 02:38:09.145772]: Done. -#> ℹ [2024-03-08 02:38:09.147158]: 0.308 secs elapsed. -#> ℹ [2024-03-08 02:38:09.15254]: Started. -#> ✔ [2024-03-08 02:38:09.153952]: Single sample mode enabled. -#> ✔ [2024-03-08 02:38:09.156173]: Done. -#> ℹ [2024-03-08 02:38:09.157571]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:38:09.158956]: Started. -#> ✔ [2024-03-08 02:38:09.160279]: Batch mode enabled. -#> ✔ [2024-03-08 02:38:09.163087]: Done. -#> ℹ [2024-03-08 02:38:09.164474]: 0.005 secs elapsed. +#> ✔ [2024-03-13 10:53:40.504204]: Signature exposures collected. +#> ✔ [2024-03-13 10:53:40.505731]: Errors and similarity collected. +#> ✔ [2024-03-13 10:53:40.507181]: Done. +#> ℹ [2024-03-13 10:53:40.50872]: 0.312 secs elapsed. +#> ℹ [2024-03-13 10:53:40.514618]: Started. +#> ✔ [2024-03-13 10:53:40.516184]: Single sample mode enabled. +#> ✔ [2024-03-13 10:53:40.518589]: Done. +#> ℹ [2024-03-13 10:53:40.520125]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:53:40.521586]: Started. +#> ✔ [2024-03-13 10:53:40.522996]: Batch mode enabled. +#> ✔ [2024-03-13 10:53:40.52598]: Done. +#> ℹ [2024-03-13 10:53:40.52752]: 0.006 secs elapsed. #> $samp1 #> threshold_0.01 threshold_0.05 threshold_0.1 diff --git a/reference/sig_fit_bootstrap_batch.html b/reference/sig_fit_bootstrap_batch.html index ee69f9f4..b19dd72d 100644 --- a/reference/sig_fit_bootstrap_batch.html +++ b/reference/sig_fit_bootstrap_batch.html @@ -160,58 +160,58 @@

Examples

z10 <- sig_fit_bootstrap_batch(V, sig = W, n = 10) z10 } -#> ℹ [2024-03-08 02:38:09.514772]: Batch Bootstrap Signature Exposure Analysis Started. -#> ℹ [2024-03-08 02:38:09.516479]: Samples to be filtered out: -#> ℹ [2024-03-08 02:38:09.517819]: Finding optimal exposures (&errors) for different methods. -#> ℹ [2024-03-08 02:38:09.519165]: Calling method `QP`. -#> ℹ [2024-03-08 02:38:09.522385]: Started. -#> ℹ [2024-03-08 02:38:09.523741]: Signature index not detected. -#> ✔ [2024-03-08 02:38:09.525086]: Signature matrix/data.frame detected. -#> ✔ [2024-03-08 02:38:09.526413]: Database and index checked. -#> ✔ [2024-03-08 02:38:09.527812]: Signature normalized. -#> ℹ [2024-03-08 02:38:09.529127]: Checking row number for catalog matrix and signature matrix. -#> ✔ [2024-03-08 02:38:09.530432]: Checked. -#> ✔ [2024-03-08 02:38:09.531758]: Method 'QP' detected. -#> ✔ [2024-03-08 02:38:09.533045]: Corresponding function generated. -#> ℹ [2024-03-08 02:38:09.534325]: Calling function. -#> ℹ [2024-03-08 02:38:09.535806]: Fitting sample: samp1 -#> ℹ [2024-03-08 02:38:09.537311]: Fitting sample: samp2 -#> ℹ [2024-03-08 02:38:09.538697]: Fitting sample: samp3 -#> ℹ [2024-03-08 02:38:09.540098]: Fitting sample: samp4 -#> ✔ [2024-03-08 02:38:09.541476]: Done. -#> ℹ [2024-03-08 02:38:09.542778]: Generating output signature exposures. -#> ✔ [2024-03-08 02:38:09.552593]: Done. -#> ℹ [2024-03-08 02:38:09.553962]: Calculating errors (Frobenius Norm). -#> ✔ [2024-03-08 02:38:09.555431]: Done. -#> ℹ [2024-03-08 02:38:09.556846]: 0.034 secs elapsed. -#> ℹ [2024-03-08 02:38:09.559659]: Getting bootstrap exposures (&errors/similarity) for different methods. -#> ℹ [2024-03-08 02:38:09.561032]: This step is time consuming, please be patient. -#> ℹ [2024-03-08 02:38:09.562471]: Processing sample `samp1`. -#> ℹ [2024-03-08 02:38:10.616621]: Processing sample `samp2`. -#> ℹ [2024-03-08 02:38:11.646391]: Processing sample `samp3`. -#> ℹ [2024-03-08 02:38:12.666762]: Processing sample `samp4`. -#> ✔ [2024-03-08 02:38:13.692074]: Gotten. -#> ℹ [2024-03-08 02:38:13.694492]: Reporting p values... -#> ℹ [2024-03-08 02:38:13.696216]: Started. -#> ✔ [2024-03-08 02:38:13.697628]: Batch mode enabled. -#> ✔ [2024-03-08 02:38:13.699567]: Done. -#> ℹ [2024-03-08 02:38:13.700973]: 0.005 secs elapsed. -#> ℹ [2024-03-08 02:38:13.702358]: Started. -#> ✔ [2024-03-08 02:38:13.703771]: Batch mode enabled. -#> ✔ [2024-03-08 02:38:13.705415]: Done. -#> ℹ [2024-03-08 02:38:13.706784]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:38:13.708164]: Started. -#> ✔ [2024-03-08 02:38:13.709472]: Batch mode enabled. -#> ✔ [2024-03-08 02:38:13.711116]: Done. -#> ℹ [2024-03-08 02:38:13.712484]: 0.004 secs elapsed. -#> ℹ [2024-03-08 02:38:13.713838]: Started. -#> ✔ [2024-03-08 02:38:13.715183]: Batch mode enabled. -#> ✔ [2024-03-08 02:38:13.716828]: Done. -#> ℹ [2024-03-08 02:38:13.718195]: 0.004 secs elapsed. -#> ✔ [2024-03-08 02:38:13.719583]: Done. -#> ℹ [2024-03-08 02:38:13.720901]: Cleaning results... -#> ✔ [2024-03-08 02:38:13.755541]: Outputing. -#> ℹ [2024-03-08 02:38:13.75742]: Total 4.243 secs elapsed. +#> ℹ [2024-03-13 10:53:40.941433]: Batch Bootstrap Signature Exposure Analysis Started. +#> ℹ [2024-03-13 10:53:40.943243]: Samples to be filtered out: +#> ℹ [2024-03-13 10:53:40.944718]: Finding optimal exposures (&errors) for different methods. +#> ℹ [2024-03-13 10:53:40.946119]: Calling method `QP`. +#> ℹ [2024-03-13 10:53:40.949574]: Started. +#> ℹ [2024-03-13 10:53:40.950994]: Signature index not detected. +#> ✔ [2024-03-13 10:53:40.952474]: Signature matrix/data.frame detected. +#> ✔ [2024-03-13 10:53:40.953917]: Database and index checked. +#> ✔ [2024-03-13 10:53:40.955455]: Signature normalized. +#> ℹ [2024-03-13 10:53:40.956878]: Checking row number for catalog matrix and signature matrix. +#> ✔ [2024-03-13 10:53:40.958301]: Checked. +#> ✔ [2024-03-13 10:53:40.959737]: Method 'QP' detected. +#> ✔ [2024-03-13 10:53:40.961124]: Corresponding function generated. +#> ℹ [2024-03-13 10:53:40.962498]: Calling function. +#> ℹ [2024-03-13 10:53:40.964167]: Fitting sample: samp1 +#> ℹ [2024-03-13 10:53:40.965707]: Fitting sample: samp2 +#> ℹ [2024-03-13 10:53:40.96716]: Fitting sample: samp3 +#> ℹ [2024-03-13 10:53:40.968673]: Fitting sample: samp4 +#> ✔ [2024-03-13 10:53:40.970194]: Done. +#> ℹ [2024-03-13 10:53:40.971603]: Generating output signature exposures. +#> ✔ [2024-03-13 10:53:40.981682]: Done. +#> ℹ [2024-03-13 10:53:40.983498]: Calculating errors (Frobenius Norm). +#> ✔ [2024-03-13 10:53:40.985112]: Done. +#> ℹ [2024-03-13 10:53:40.986586]: 0.037 secs elapsed. +#> ℹ [2024-03-13 10:53:40.989764]: Getting bootstrap exposures (&errors/similarity) for different methods. +#> ℹ [2024-03-13 10:53:40.991318]: This step is time consuming, please be patient. +#> ℹ [2024-03-13 10:53:40.992906]: Processing sample `samp1`. +#> ℹ [2024-03-13 10:53:42.363115]: Processing sample `samp2`. +#> ℹ [2024-03-13 10:53:43.686993]: Processing sample `samp3`. +#> ℹ [2024-03-13 10:53:44.988836]: Processing sample `samp4`. +#> ✔ [2024-03-13 10:53:46.304427]: Gotten. +#> ℹ [2024-03-13 10:53:46.306904]: Reporting p values... +#> ℹ [2024-03-13 10:53:46.308464]: Started. +#> ✔ [2024-03-13 10:53:46.309855]: Batch mode enabled. +#> ✔ [2024-03-13 10:53:46.311711]: Done. +#> ℹ [2024-03-13 10:53:46.313145]: 0.005 secs elapsed. +#> ℹ [2024-03-13 10:53:46.314551]: Started. +#> ✔ [2024-03-13 10:53:46.31592]: Batch mode enabled. +#> ✔ [2024-03-13 10:53:46.317611]: Done. +#> ℹ [2024-03-13 10:53:46.319018]: 0.004 secs elapsed. +#> ℹ [2024-03-13 10:53:46.320452]: Started. +#> ✔ [2024-03-13 10:53:46.321821]: Batch mode enabled. +#> ✔ [2024-03-13 10:53:46.32355]: Done. +#> ℹ [2024-03-13 10:53:46.324952]: 0.004 secs elapsed. +#> ℹ [2024-03-13 10:53:46.326346]: Started. +#> ✔ [2024-03-13 10:53:46.32773]: Batch mode enabled. +#> ✔ [2024-03-13 10:53:46.329414]: Done. +#> ℹ [2024-03-13 10:53:46.330814]: 0.004 secs elapsed. +#> ✔ [2024-03-13 10:53:46.332257]: Done. +#> ℹ [2024-03-13 10:53:46.333606]: Cleaning results... +#> ✔ [2024-03-13 10:53:46.369149]: Outputing. +#> ℹ [2024-03-13 10:53:46.371498]: Total 5.43 secs elapsed. #> $expo #> method sample sig exposure type #> <char> <char> <fctr> <num> <char> diff --git a/reference/sig_tally.html b/reference/sig_tally.html index 63733553..9538718b 100644 --- a/reference/sig_tally.html +++ b/reference/sig_tally.html @@ -243,24 +243,24 @@

Examples

# \donttest{ # Use method designed by Wang, Shixiang et al. cn_tally_W <- sig_tally(cn, method = "W") -#> ℹ [2024-03-08 02:38:14.235257]: Started. -#> ℹ [2024-03-08 02:38:14.238539]: Step: getting copy number features. -#> ℹ [2024-03-08 02:38:14.263241]: Getting breakpoint count per 10 Mb... -#> ℹ [2024-03-08 02:38:14.486288]: Getting breakpoint count per chromosome arm... -#> ℹ [2024-03-08 02:38:14.662729]: Getting copy number... -#> ℹ [2024-03-08 02:38:14.669422]: Getting change-point copy number change... -#> ℹ [2024-03-08 02:38:14.804461]: Getting length of chains of oscillating copy number... -#> ℹ [2024-03-08 02:38:14.939884]: Getting (log10 based) segment size... -#> ℹ [2024-03-08 02:38:14.94677]: Getting the minimal number of chromosome with 50% CNV... -#> ℹ [2024-03-08 02:38:15.013917]: Getting burden of chromosome... -#> ✔ [2024-03-08 02:38:15.028405]: Gotten. -#> ℹ [2024-03-08 02:38:15.02987]: Step: generating copy number components. -#> ✔ [2024-03-08 02:38:15.031243]: `feature_setting` checked. -#> ℹ [2024-03-08 02:38:15.034567]: Step: counting components. -#> ✔ [2024-03-08 02:38:15.327817]: Counted. -#> ℹ [2024-03-08 02:38:15.329769]: Step: generating components by sample matrix. -#> ✔ [2024-03-08 02:38:15.331983]: Matrix generated. -#> ℹ [2024-03-08 02:38:15.333425]: 1.098 secs elapsed. +#> ℹ [2024-03-13 10:53:46.962193]: Started. +#> ℹ [2024-03-13 10:53:46.965808]: Step: getting copy number features. +#> ℹ [2024-03-13 10:53:46.994985]: Getting breakpoint count per 10 Mb... +#> ℹ [2024-03-13 10:53:47.260406]: Getting breakpoint count per chromosome arm... +#> ℹ [2024-03-13 10:53:47.437491]: Getting copy number... +#> ℹ [2024-03-13 10:53:47.445114]: Getting change-point copy number change... +#> ℹ [2024-03-13 10:53:47.592673]: Getting length of chains of oscillating copy number... +#> ℹ [2024-03-13 10:53:47.741307]: Getting (log10 based) segment size... +#> ℹ [2024-03-13 10:53:47.748866]: Getting the minimal number of chromosome with 50% CNV... +#> ℹ [2024-03-13 10:53:47.825438]: Getting burden of chromosome... +#> ✔ [2024-03-13 10:53:47.841615]: Gotten. +#> ℹ [2024-03-13 10:53:47.843478]: Step: generating copy number components. +#> ✔ [2024-03-13 10:53:47.845169]: `feature_setting` checked. +#> ℹ [2024-03-13 10:53:47.84888]: Step: counting components. +#> ✔ [2024-03-13 10:53:48.180823]: Counted. +#> ℹ [2024-03-13 10:53:48.183122]: Step: generating components by sample matrix. +#> ✔ [2024-03-13 10:53:48.186218]: Matrix generated. +#> ℹ [2024-03-13 10:53:48.188205]: 1.226 secs elapsed. # } # Use method designed by Steele et al. # See example in read_copynumber @@ -274,7 +274,7 @@

Examples

#> -Summarizing #> -Processing clinical data #> --Missing clinical data -#> -Finished in 0.181s elapsed (0.226s cpu) +#> -Finished in 0.191s elapsed (0.237s cpu) if (require("BSgenome.Hsapiens.UCSC.hg19")) { mt_tally <- sig_tally( laml, @@ -295,53 +295,53 @@

Examples

} else { message("Please install package 'BSgenome.Hsapiens.UCSC.hg19' firstly!") } -#> ℹ [2024-03-08 02:38:15.518982]: Started. -#> ℹ [2024-03-08 02:38:15.523166]: We would assume you marked all variants' position in + strand. -#> ✔ [2024-03-08 02:38:15.524861]: Reference genome loaded. -#> ✔ [2024-03-08 02:38:15.529161]: Variants from MAF object queried. -#> ✔ [2024-03-08 02:38:15.531485]: Chromosome names checked. -#> ✔ [2024-03-08 02:38:15.534678]: Sex chromosomes properly handled. -#> ✔ [2024-03-08 02:38:15.536285]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. -#> ✔ [2024-03-08 02:38:15.541265]: Variant start and end position checked. -#> ✔ [2024-03-08 02:38:15.545048]: Variant data for matrix generation preprocessed. -#> ℹ [2024-03-08 02:38:15.546418]: SBS matrix generation - start. -#> ℹ [2024-03-08 02:38:15.548243]: Extracting 5' and 3' adjacent bases. -#> ℹ [2024-03-08 02:38:15.840122]: Extracting +/- 20bp around mutated bases for background C>T estimation. -#> ℹ [2024-03-08 02:38:16.166037]: Estimating APOBEC enrichment scores. -#> ℹ [2024-03-08 02:38:16.167985]: Performing one-way Fisher's test for APOBEC enrichment. -#> ✔ [2024-03-08 02:38:16.258805]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) -#> ℹ [2024-03-08 02:38:16.262671]: Creating SBS sample-by-component matrices. -#> ✔ [2024-03-08 02:38:16.267077]: SBS-6 matrix created. -#> ✔ [2024-03-08 02:38:16.271943]: SBS-96 matrix created. -#> ✔ [2024-03-08 02:38:16.286035]: SBS-1536 matrix created. -#> ℹ [2024-03-08 02:38:16.287497]: Return SBS-96 as major matrix. -#> ✔ [2024-03-08 02:38:16.289968]: Done. -#> ℹ [2024-03-08 02:38:16.291413]: 0.772 secs elapsed. -#> ℹ [2024-03-08 02:38:16.292813]: Started. -#> ℹ [2024-03-08 02:38:16.29659]: We would assume you marked all variants' position in + strand. -#> ✔ [2024-03-08 02:38:16.298289]: Reference genome loaded. -#> ✔ [2024-03-08 02:38:16.302629]: Variants from MAF object queried. -#> ✔ [2024-03-08 02:38:16.304985]: Chromosome names checked. -#> ✔ [2024-03-08 02:38:16.30819]: Sex chromosomes properly handled. -#> ✔ [2024-03-08 02:38:16.309803]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. -#> ✔ [2024-03-08 02:38:16.314773]: Variant start and end position checked. -#> ✔ [2024-03-08 02:38:16.318644]: Variant data for matrix generation preprocessed. -#> ℹ [2024-03-08 02:38:16.320057]: SBS matrix generation - start. -#> ℹ [2024-03-08 02:38:16.321862]: Extracting 5' and 3' adjacent bases. -#> ℹ [2024-03-08 02:38:16.606259]: Extracting +/- 20bp around mutated bases for background C>T estimation. -#> ℹ [2024-03-08 02:38:16.941859]: Estimating APOBEC enrichment scores. -#> ℹ [2024-03-08 02:38:16.943795]: Performing one-way Fisher's test for APOBEC enrichment. -#> ✔ [2024-03-08 02:38:17.017725]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) -#> ℹ [2024-03-08 02:38:17.02123]: Creating SBS sample-by-component matrices. -#> ✔ [2024-03-08 02:38:17.025584]: SBS-6 matrix created. -#> ✔ [2024-03-08 02:38:17.030461]: SBS-96 matrix created. -#> ✔ [2024-03-08 02:38:17.044602]: SBS-1536 matrix created. -#> ✔ [2024-03-08 02:38:17.08764]: SBS-24 (6x4) matrix created. -#> ✔ [2024-03-08 02:38:17.13188]: SBS-384 (96x4) matrix created. -#> ✔ [2024-03-08 02:38:17.25113]: SBS-6144 (1536x4) matrix created. -#> ℹ [2024-03-08 02:38:17.253041]: Return SBS-192 as major matrix. -#> ✔ [2024-03-08 02:38:17.261213]: Done. -#> ℹ [2024-03-08 02:38:17.262669]: 0.97 secs elapsed. +#> ℹ [2024-03-13 10:53:48.384378]: Started. +#> ℹ [2024-03-13 10:53:48.388958]: We would assume you marked all variants' position in + strand. +#> ✔ [2024-03-13 10:53:48.391051]: Reference genome loaded. +#> ✔ [2024-03-13 10:53:48.395989]: Variants from MAF object queried. +#> ✔ [2024-03-13 10:53:48.398562]: Chromosome names checked. +#> ✔ [2024-03-13 10:53:48.402093]: Sex chromosomes properly handled. +#> ✔ [2024-03-13 10:53:48.40397]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. +#> ✔ [2024-03-13 10:53:48.409205]: Variant start and end position checked. +#> ✔ [2024-03-13 10:53:48.413469]: Variant data for matrix generation preprocessed. +#> ℹ [2024-03-13 10:53:48.414977]: SBS matrix generation - start. +#> ℹ [2024-03-13 10:53:48.417105]: Extracting 5' and 3' adjacent bases. +#> ℹ [2024-03-13 10:53:48.743473]: Extracting +/- 20bp around mutated bases for background C>T estimation. +#> ℹ [2024-03-13 10:53:49.151433]: Estimating APOBEC enrichment scores. +#> ℹ [2024-03-13 10:53:49.153552]: Performing one-way Fisher's test for APOBEC enrichment. +#> ✔ [2024-03-13 10:53:49.230558]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) +#> ℹ [2024-03-13 10:53:49.23435]: Creating SBS sample-by-component matrices. +#> ✔ [2024-03-13 10:53:49.239156]: SBS-6 matrix created. +#> ✔ [2024-03-13 10:53:49.244447]: SBS-96 matrix created. +#> ✔ [2024-03-13 10:53:49.260556]: SBS-1536 matrix created. +#> ℹ [2024-03-13 10:53:49.262692]: Return SBS-96 as major matrix. +#> ✔ [2024-03-13 10:53:49.265692]: Done. +#> ℹ [2024-03-13 10:53:49.26755]: 0.883 secs elapsed. +#> ℹ [2024-03-13 10:53:49.269277]: Started. +#> ℹ [2024-03-13 10:53:49.273544]: We would assume you marked all variants' position in + strand. +#> ✔ [2024-03-13 10:53:49.275681]: Reference genome loaded. +#> ✔ [2024-03-13 10:53:49.280721]: Variants from MAF object queried. +#> ✔ [2024-03-13 10:53:49.283594]: Chromosome names checked. +#> ✔ [2024-03-13 10:53:49.287324]: Sex chromosomes properly handled. +#> ✔ [2024-03-13 10:53:49.289629]: Only variants located in standard chromosomes (1:22, X, Y, M/MT) are kept. +#> ✔ [2024-03-13 10:53:49.295524]: Variant start and end position checked. +#> ✔ [2024-03-13 10:53:49.301136]: Variant data for matrix generation preprocessed. +#> ℹ [2024-03-13 10:53:49.30315]: SBS matrix generation - start. +#> ℹ [2024-03-13 10:53:49.305707]: Extracting 5' and 3' adjacent bases. +#> ℹ [2024-03-13 10:53:49.688189]: Extracting +/- 20bp around mutated bases for background C>T estimation. +#> ℹ [2024-03-13 10:53:50.066149]: Estimating APOBEC enrichment scores. +#> ℹ [2024-03-13 10:53:50.068179]: Performing one-way Fisher's test for APOBEC enrichment. +#> ✔ [2024-03-13 10:53:50.143516]: APOBEC related mutations are enriched in 3.297% of samples (APOBEC enrichment score > 2; 6 of 182 samples) +#> ℹ [2024-03-13 10:53:50.147157]: Creating SBS sample-by-component matrices. +#> ✔ [2024-03-13 10:53:50.151805]: SBS-6 matrix created. +#> ✔ [2024-03-13 10:53:50.157109]: SBS-96 matrix created. +#> ✔ [2024-03-13 10:53:50.171888]: SBS-1536 matrix created. +#> ✔ [2024-03-13 10:53:50.218352]: SBS-24 (6x4) matrix created. +#> ✔ [2024-03-13 10:53:50.267709]: SBS-384 (96x4) matrix created. +#> ✔ [2024-03-13 10:53:50.395082]: SBS-6144 (1536x4) matrix created. +#> ℹ [2024-03-13 10:53:50.397084]: Return SBS-192 as major matrix. +#> ✔ [2024-03-13 10:53:50.404902]: Done. +#> ℹ [2024-03-13 10:53:50.40665]: 1.137 secs elapsed. #> sample component N_T N_U Total_T Total_U Enrichment p_value #> <char> <char> <int> <int> <int> <int> <num> <num> #> 1: TCGA-AB-2838 C>T 3 7 12 8 0.4285714 0.01976661 diff --git a/reference/sigminer-package.html b/reference/sigminer-package.html index c4746479..5c0bac42 100644 --- a/reference/sigminer-package.html +++ b/reference/sigminer-package.html @@ -84,6 +84,8 @@

sigminer: Extract, Analyze and Visualize Signatures for Genomic Variations

See also

Useful links: