extractSigsSv: Extract structural variant signatures

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

Extract structural variant signatures

Description

Will return 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.

To elaborate, the 6 SV signatures used are those described in this paper: https://media.nature.com/original/nature-assets/nature/journal/v534/n7605/extref/nature17676-s3.zip, in Supplementary.Table.21.Signatures.v3.xlsx. These are derived from mutation contexts composed of SV type/length.

Note that the probabilities of the clustered and non-clustered rearrangements in the signature profile have been combined. In other words, whether the rearrangements were clustered/non-clustered were not considered.

Usage

extractSigsSv(
  vcf.file = NULL,
  df = NULL,
  output = "signatures",
  sample.name = NULL,
  sv.caller = "gridss",
  half.tra.counts = F,
  sv.len.cutoffs = if (output == "signatures") {     c(10^c(3:7), Inf) } else {    
    c(0, 10^c(3:7), Inf) },
  signature.profiles = SV_SIGNATURE_PROFILES,
  verbose = F,
  ...
)

Arguments

vcf.file	Path to the vcf file
df	A dataframe with the columns: sv_type, sv_len. sv_type can be DEL, DUP, INV, TRA, BND. Note that for TRA and BND, sv_len will be ignored. Alternative input option to vcf.file
output	Output the absolute signature contributions (default, 'signatures'), or the SV type/length contexts ('contexts')
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.
sv.caller	Can be 'manta', 'gridss', or 'pcawg'
half.tra.counts	Divide translocation counts by 2?
sv.len.cutoffs	SV length cutoff intervals as a numeric vector.
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.