CheckAndReturnIDMatrix: Check and return the ID mutation matrix

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

Check and return the ID mutation matrix

Description

Check and return the ID mutation matrix

Usage

CheckAndReturnIDMatrix(
  annotated.vcf,
  discarded.variants,
  ID.mat,
  return.annotated.vcf = FALSE
)

Arguments

annotated.vcf	An annotated ID VCF with additional column ID.class showing ID classification for each variant.
discarded.variants	A data.frame which contains rows of ID variants which are excluded in the analysis.
ID.mat	The ID mutation count matrix.
return.annotated.vcf	Whether to return annotated.vcf. Default is FALSE.

Value

A list of a 1-column ID matrix containing the mutation catalog information and the annotated VCF with ID categories information added. If some ID variants were excluded in the analysis, an additional element discarded.variants will appear in the return list.

ICAMS documentation built on June 22, 2024, 6:47 p.m.