ReadMutectVCFs: Read Mutect VCF files.

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

Description

Read Mutect VCF files.

Usage

ReadMutectVCFs(files, names.of.VCFs = NULL, tumor.col.names = NA)

Arguments

files	Character vector of file paths to the VCF files.
names.of.VCFs	Character vector of names of the VCF files. The order of names in names.of.VCFs should match the order of VCF file paths in files. If NULL(default), this function will remove all of the path up to and including the last path separator (if any) in files and file paths without extensions (and the leading dot) will be used as the names of the VCF files.
tumor.col.names	Character vector of column names in VCFs which contain the tumor sample information. The order of names in tumor.col.names should match the order of VCFs specified in files. If tumor.col.names is equal to NA(default), this function will use the 10th column in all the VCFs to calculate VAFs. See GetMutectVAF for more details.

Value

A list of data frames which store data lines of VCF files with two additional columns added which contain the VAF(variant allele frequency) and read depth information.

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