CheckAndReturnSBSMatrix: Check and return the SBS mutation matrix

Description

Check and return the SBS mutation matrix

Usage

CheckAndReturnSBSMatrix(
  vcf,
  discarded.variants,
  mat96,
  mat1536,
  mat192 = NULL,
  return.annotated.vcf = FALSE,
  sample.id = "counts"
)

Value

A list of three 1-column matrices with the names catSBS96, catSBS192, catSBS1536. If transcript information is not available in vcf, catSBS192 is not generated. Do not rely on the order of elements in the list. If return.annotated.vcf = TRUE, another element annotated.vcf will appear in the list. If there are SBS variants whose pentanucleotide context contains "N", they will be excluded in the analysis and an additional element discarded.variants will appear in the return list.

Arguments

vcf: An in-memory VCF file annotated with sequence context and transcript information by function AnnotateSBSVCF. It must *not* contain indels and must *not* contain DBS (double base substitutions), or triplet base substitutions etc., even if encoded as neighboring SBS.
discarded.variants: A data.frame which contains rows of SBS variants whose pentanucleotide context contains "N".
mat96: The SBS96 mutation count matrix.
mat1536: The SBS1536 mutation count matrix.
mat192: The SBS192 mutation count matrix.
return.annotated.vcf: Whether to return the annotated VCF with additional columns showing the mutation class for each variant. Default is FALSE.
sample.id: Usually the sample id, but defaults to "count".