vcfToSNVcatalogue: VCF to SNV catalogue

In pdiakumis/hrdetect: Signature Tools

Description

Convert a vcf file containing SNV to SNV 96 channel trinuclotide context catalogue. The VCF file should containt the SNV of a single sample.

Usage

vcfToSNVcatalogue(vcfFilename, genome.v = "hg19")

Arguments

vcfFilename	path to input VCF (file must be tabix indexed)
genome.v	either "hg38" (will load BSgenome.Hsapiens.UCSC.hg38), "hg19" (will load BSgenome.Hsapiens.1000genomes.hs37d5), mm10 (will load BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10) or canFam3 (will load BSgenome.Cfamiliaris.UCSC.canFam3::BSgenome.Cfamiliaris.UCSC.canFam3)

Value

returns the SNV catalogue for the given sample

Examples

file_subs <- "subs.vcf"
res <- vcfToSNVcatalogue(file_subs,genome.v = "hg38")

pdiakumis/hrdetect documentation built on May 17, 2020, 5:30 p.m.