tabToSNVcatalogue: TAB to SNV Catalogue

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

TAB to SNV Catalogue

Description

Convert a data frame containing SNV, possibly loaded from a tab seperated text file, to SNV 96 channel trinuclotide context catalogue. The data frame should containt the SNV of a single sample, and the following minimal columns: chr, position, REF, ALT.

Usage

tabToSNVcatalogue(subs, genome.v = "hg19")

Arguments

subs	data frame with subs from a single sample and the following minimal columns: chr, position, REF, ALT.
genome.v	either "hg38" (will load BSgenome.Hsapiens.NCBI.GRCh38), "hg19" (will load BSgenome.Hsapiens.UCSC.hg19), 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

subs <- read.table("subs.tab",sep="\t",header = TRUE,check.names = FALSE,stringsAsFactors = FALSE)
res <- tabToSNVcatalogue(subs,genome.v = "hg19")

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.