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R
ICAMS

CheckAndReturnIDMatrix

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

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

v2.3.10
GPL-3 | file LICENSE
Authors
Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu
Initial release

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