GetMutationLoadsFromMutectVCFs: Get mutation loads information from Mutect VCF files.

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

Description

Get mutation loads information from Mutect VCF files.

Usage

GetMutationLoadsFromMutectVCFs(catalogs)

Arguments

catalogs

A list generated by calling function MutectVCFFilesToCatalog to Mutect VCF files.

Value

A list containing mutation loads information from Mutect VCF files:

1. total.variants Total number of mutations.

2. SBS Number of single base substitutions.

3. DBS Number of double base substitutions.

4. ID Number of small insertions and deletions.

5. discarded.variants Number of other types of mutations which are excluded in the analysis in ICAMS.

ICAMS documentation built on April 3, 2021, 5:07 p.m.