sampleStrandBias: Transcription and Replication strand bias for a sample

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

Transcription and Replication strand bias for a sample

Description

This function computes the transcription/replication strand bias of a given set of single base substitutions, typically from a single sample. The function returns the bias of the mutations with and without the trinucleotide context.

Usage

sampleStrandBias(snv_table, genomev = "hg19")

Arguments

snv_table	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

strand bias results

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