fix #445

ShixiangWang · Dec 5, 2023 · 313abe2 · 313abe2
1 parent 1593f0b
commit 313abe2
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diff --git a/NEWS.md b/NEWS.md
@@ -7,6 +7,8 @@ get_sig_db("latest_RNA-SBS_GRCh37")
 get_sig_db("latest_SV_GRCh38")
 ```
 
+- Fixed a bug in generating matrix for variation categories with strand bias due to problematic counting. (#445)
+
 # sigminer 2.2.2
 
 - Updated pkg doc following the new CRAN feature (thanks to K from the CRAN team).

diff --git a/R/generate_matrices.R b/R/generate_matrices.R
@@ -701,7 +701,7 @@ records_to_matrix <- function(dt, samp_col, component_col, add_trans_bias = FALS
     loc_dt$MutIndex <- 1:nrow(loc_dt)
 
     m_dt <- data.table::foverlaps(loc_dt, transcript_dt, type = "any")[
-      , .(MatchCount = .N, strand = paste0(unique(strand), collapse = "/")),
+      , .(MatchCount = length(unique(strand)), strand = paste0(unique(strand), collapse = "/")),
       by = list(MutIndex)
     ]
 

diff --git a/R/read_vcf.R b/R/read_vcf.R
@@ -21,7 +21,7 @@
 #' @testexamples
 #' expect_is(maf, "MAF")
 read_vcf <- function(vcfs, samples = NULL,
-                     genome_build = c("hg19", "hg38", "mm10", "mm9", "ce11"),
+                     genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11"),
                      keep_only_pass = FALSE, verbose = TRUE) {
   genome_build <- match.arg(genome_build)
   vcfs_name <- vcfs