updated docs

R/main.R

@@ -188,10 +188,12 @@ generate_cpsr_report <- function(yaml_fname = NULL) {
     ),
     collapse = ", "
   )
-  pcgrr::log4r_info(paste0(
-    "Variants were found in the following cancer ",
-    "predisposition genes: ", gene_hits
-  ))
+  if(nchar(gene_hits) > 0){
+    pcgrr::log4r_info(paste0(
+      "Variants were found in the following cancer ",
+      "predisposition genes: ", gene_hits
+    ))
+  }
 
   if (cps_report$content$snv_indel$v_stat_sf$n > 0) {
     sf_hits <- paste(
@@ -212,7 +214,7 @@ generate_cpsr_report <- function(yaml_fname = NULL) {
     )
 
   pcgrr::log4r_info(
-    "Generating hyperlinked annotations for output data frames"
+    "Generating hyperlinked annotations for output data tables"
   )
   for (c in c("sf", "cpg_non_sf", "gwas", "bm")) {
     if (NROW(

inst/templates/quarto/cpsr_gwas.qmd

@@ -2,7 +2,9 @@
 
 <br>
 
-```{r prepare_gwas_data, echo=F, results='asis'}
+```{r prepare_gwas_data}
+#| echo: false
+#| results: asis
 
 show_gwas_filters <- F
 missing_gwas_items <- T
@@ -13,7 +15,10 @@ if (NROW(cps_report[["content"]][["snv_indel"]]$callset$variant_display$gwas) >
 
 ```
 
-```{r gwas_cancer, echo=F, results = 'asis', eval = show_gwas_filters}
+```{r gwas_cancer}
+#| echo: false
+#| results: asis
+#| eval: !expr show_gwas_filters
 
 cat("A total of N = <b>", NROW(cps_report[["content"]][["snv_indel"]]$callset$variant_display$gwas), "</b> other germline variant(s) in the query VCF are associated with cancer phenotypes, as found through [genome-wide association studies](https://www.ebi.ac.uk/gwas/):")
 cat("\n")
@@ -56,7 +61,11 @@ DT::datatable(variants_gwas_cancer,
 # htmltools::br()
 ```
 
-```{r gwas_cancer_missing, echo=F, results = 'asis', eval = missing_gwas_items}
+```{r gwas_cancer_missing}
+#| echo: false
+#| results: asis
+#| eval: !expr missing_gwas_items
+
 cat("<i><b>NO</b> GWAS tag SNPs were found beyond the variants reported in the targeted cancer predisposition genes </i>", sep = "\n")
 cat("\n")
 ```

pkgdown/index.md

@@ -10,7 +10,7 @@ The *Cancer Predisposition Sequencing Reporter (CPSR)* is a computational workfl
 
 1) Flexible **selection of cancer predisposition genes** subject to analysis and reporting - through the use of virtual gene panels
 2) **Variant classification** (*Pathogenic* to _Benign_) through a dedicated implementation of [ACMG/AMP guidelines](https://pubmed.ncbi.nlm.nih.gov/25741868/)
-3) **Detection of germline biomarkers** - for prognosis, diagnosis, or drug sensitivity/resistance
+3) **Detection of germline biomarkers** - for prognosis, diagnosis, or drug sensitivity/resistance in cancer
 4) Reporting of **secondary/incidental findings** ([ACMG recommendations](https://pubmed.ncbi.nlm.nih.gov/37347242/))
 5) **Interactive HTML output report** with detailed variant information, gene annotations, and external links to relevant databases
 
@@ -25,9 +25,15 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 
 ### News
 
+
+* *September 2024*: **2.1.0 release**
+  - data bundle upgrade
+  - re-calibration of classification tresholds
+  - [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
+
 * *August 2024*: **2.0.3 release**
-    - patch with bug fix for copying in quarto templates ([pr62](https://github.com/sigven/cpsr/pull/62))
-    - [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
+  - patch with bug fix for copying in quarto templates ([pr62](https://github.com/sigven/cpsr/pull/62))
+  - [CHANGELOG](https://sigven.github.io/cpsr/articles/CHANGELOG.html)
 
 * *July 2024*: **2.0.1 release**
   - patch with bug fix for mitochondrial input variants ([pr245](https://github.com/sigven/pcgr/pull/245))
@@ -43,16 +49,10 @@ Snapshots of sections in the [quarto](https://quarto.org)-based cancer predispos
 * *November 2022*: **1.0.1 release**
   * Added CPSR logo (designed by [Hal Nakken](https://halvetica.net))
 
-* *February 2022*: **1.0.0 release**
-  * Complete restructure of code and Conda installation routines, contributed largely by the great [@pdiakumis](https://github.com/pdiakumis)
-  * Updated bundle (ClinVar, CancerMine, UniprotKB, PanelApp, CIViC, GWAS catalog)
-  * Software upgrade (VEP, R/BioConductor)
-  * New documentation site (https://sigven.github.io/cpsr)
-
 
 ### Example report
 
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.12734384.svg)](https://doi.org/10.5281/zenodo.12734384)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13855978.svg)](https://doi.org/10.5281/zenodo.13855978)
 
 ### Getting started
 

vignettes/CHANGELOG.Rmd

@@ -3,6 +3,17 @@ title: "Changelog"
 output: rmarkdown::html_document
 ---
 
+## v2.1.0
+
+- Date: **2024-09-29**
+- Major data updates
+  - ClinVar (2024-09)
+  - dbNSFP (v4.8)
+  - CIViC (2024-09-18)
+- Adjusted thresholds for CPSR variant classification based on calibration against ClinVar (Sept 2024 release)
+- Added link to chosen virtual panel in HTML report
+- Created new column `ALTERATION` in variant tables of HTML report, a joint annotation of `HGVSp` and `HGVSc`
+
 ## v2.0.3
 
 - Date: **2024-08-01**

vignettes/annotation_resources.Rmd

@@ -7,27 +7,27 @@ output: rmarkdown::html_document
   * [VEP v112](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor ([GENCODE v46](https://www.gencodegenes.org/human/) as gene reference database (v19 for grch37))
 
 ###  *Insilico* predictions of effect of coding variants
-  * [dBNSFP](https://sites.google.com/site/jpopgen/dbNSFP) - database of non-synonymous functional predictions (v4.5, November 2023)
+  * [dBNSFP](https://sites.google.com/site/jpopgen/dbNSFP) - database of non-synonymous functional predictions (v4.8, June 2024)
 
 ###  Variant frequency databases
   * [gnomAD](http://exac.broadinstitute.org/) - germline variant frequencies exome-wide (r2.1, October 2018)
   * [dbSNP](http://www.ncbi.nlm.nih.gov/SNP/) - database of short genetic variants (build 154)
   * [Cancer Hotspots](http://cancerhotspots.org) - a resource for statistically significant mutations in cancer (v2, 2017)
 
 ### Variant databases of clinical utility
-  * [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - database of clinically related variants (June 2024)
-  * [CIViC](https://civicdb.org) - clinical interpretations of variants in cancer (June 21st 2024)
+  * [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/) - database of clinically related variants (September 2024)
+  * [CIViC](https://civicdb.org) - clinical interpretations of variants in cancer (September 18th 2024)
 
 ### Protein domains/functional features
-  * [UniProt/SwissProt KnowledgeBase](http://www.uniprot.org) - resource on protein sequence and functional information (2024_03)
-  * [Pfam](http://pfam.xfam.org) - database of protein families and domains (v35.0, November 2021)
+  * [UniProt/SwissProt KnowledgeBase](http://www.uniprot.org) - resource on protein sequence and functional information (2024_04)
+  * [Pfam](http://pfam.xfam.org) - database of protein families and domains (v37.0)
 
 ### Cancer gene knowledge bases
   * [CancerMine](http://bionlp.bcgsc.ca/cancermine/) - Literature-mined database of tumor suppressor genes/proto-oncogenes (v50, March 2023)
-  * [Genomics England PanelApp](https://panelapp.genomicsengland.co.uk) - cancer phenotype panels as of June 2024
+  * [Genomics England PanelApp](https://panelapp.genomicsengland.co.uk) - cancer phenotype panels as of August 2024
   * [Cancer Gene Census](https://www.sanger.ac.uk/data/cancer-gene-census/) - genes implicated with cancer susceptibility (v100)
 
 ### Phenotype ontologies
-  * [UMLS/MedGen](https://www.ncbi.nlm.nih.gov/medgen/) - May 2024
-  * [Disease Ontology](https://disease-ontology.org/) - April 2024
-  * [Experimental Factor Ontology](https://github.com/EBISPOT/efo) - v3.66.0
+  * [UMLS/MedGen](https://www.ncbi.nlm.nih.gov/medgen/) - August 2024
+  * [Disease Ontology](https://disease-ontology.org/) - August 2024
+  * [Experimental Factor Ontology](https://github.com/EBISPOT/efo) - v3.69.0