R: Check and return the ID mutation matrix

CheckAndReturnIDMatrix

R Documentation

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.