Add R-Script for gene panel

Author: nr23730

genepanels/genepanel.R

@@ -0,0 +1,53 @@
+#!/usr/bin/env Rscript
+
+## ---------------------------
+##
+## Script name: bed2cBioPortalGenePanel.R
+##
+## Converts a bed file to a gene panel for cBioPortal.
+##
+## Author: Niklas Reimer, M.Sc.
+##
+## Date Created: 2020-10-30
+## Email: [email protected]
+##
+## ---------------------------
+
+require(tidyr)
+require(biomaRt)
+
+args = commandArgs(trailingOnly=TRUE)
+
+# read genes provided by cBioPortal
+cbiogenes <- read.table("cbioportal_genes.txt", header = TRUE, sep = "\t", quote="\"")
+# read provided metadata for panel
+meta <- read.table(paste0(args[1], "/meta.csv"), header = TRUE, sep=";")
+# read provided bed file
+bed <- read.table(paste0(args[1], "/target.bed"))
+
+# remove chr prefix if present
+regions <- paste(gsub("chr", "", bed$V1), paste(bed$V2, bed$V3, sep="-"), sep=":")
+
+# setup ensembl
+m <- useMart('ensembl', dataset='hsapiens_gene_ensembl')
+df <- getBM(mart=m, attributes=c('entrezgene_id'), filters=c('chromosomal_region'), values=list(c(regions)))
+
+# remove duplicate ids
+entrez <- df$entrezgene_id[!duplicated(df$entrezgene_id)]
+
+#get genes using entrez id from cbioportal dataset
+genes <- cbiogenes$HUGO_GENE_SYMBOL[!is.na(match(cbiogenes$ENTREZ_GENE_ID, entrez))]
+
+#sort genes
+genes <- sort(genes)
+
+# write to file
+sink(paste0(args[1], "/panel.txt"))
+cat(paste("stable_id", meta$stable_id, sep = ": "))
+cat("\n")
+cat(paste("description", meta$description, sep = ": "))
+cat("\n")
+
+cat("gene_list: ")
+cat(writeLines(as.character(genes), sep="\t"))
+sink()