extractSigsSnv: Extract single nucleotide variant signatures

In UMCUGenetics/mutSigExtractor: Extracts SNV, indel, DBS, and SV signatures from vcf files.

Extract single nucleotide variant signatures

Description

Will output a 1-column matrix containing: (if output=='signatures') the absolute signature contributions (i.e. the number of mutations contributing to each mutational signature), or (if output=='contexts') the mutation contexts, or (if output=='df') a dataframe with each mutation annotated by context

Usage

extractSigsSnv(
  vcf.file = NULL,
  df = NULL,
  output = "signatures",
  sample.name = NULL,
  ref.genome = DEFAULT_GENOME,
  signature.profiles = SBS_SIGNATURE_PROFILES_V2,
  verbose = F,
  ...
)

Arguments

vcf.file	Path to the vcf file
df	A dataframe containing the columns: chrom, pos, ref, alt. Alternative input option to vcf.file
output	Output the absolute signature contributions (default, 'signatures'), the 96-trinucleotide contexts ('contexts'), or an annotated bed-like dataframe ('df')
sample.name	If a character is provided, the header for the output matrix will be named to this. If none is provided, the basename of the vcf file will be used.
ref.genome	A BSgenome reference genome. Default is BSgenome.Hsapiens.UCSC.hg19. If another reference genome is indicated, it will also need to be installed.
signature.profiles	A matrix containing the mutational signature profiles, where rows are the mutation contexts and the columns are the mutational signatures.
verbose	Print progress messages?

Value

A 1-column matrix containing the context counts or signature contributions

UMCUGenetics/mutSigExtractor documentation built on Aug. 30, 2024, 2:12 p.m.