extractSigsDbs: Extract doublet substitution signatures

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

Extract doublet substitution 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

extractSigsDbs(
  vcf.file = NULL,
  df = NULL,
  output = "contexts",
  sample.name = NULL,
  signature.profiles = DBS_SIGNATURE_PROFILES,
  ref.genome = NULL,
  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 DBS 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.
signature.profiles	A matrix containing the mutational signature profiles, where rows are the mutation contexts and the columns are the mutational signatures.
ref.genome	Deprecated. Argument only kept for compatibility.
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.