ReadStrelkaIDVCFs: Read Strelka ID (small insertion and deletion) VCF files

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

Description

Read Strelka ID (small insertion and deletion) VCF files

Usage

ReadStrelkaIDVCFs(files, names.of.VCFs = NULL)

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.

Value

A list of data frames containing data lines of the VCF files.

Note

In ID (small insertion and deletion) catalogs, deletion repeat sizes range from 0 to 5+, but for plotting and end-user documentation deletion repeat sizes range from 1 to 6+.

See Also

StrelkaIDVCFFilesToCatalog

Examples

file <- c(system.file("extdata/Strelka-ID-vcf",
                      "Strelka.ID.GRCh37.s1.vcf",
                      package = "ICAMS"))
list.of.vcfs <- ReadStrelkaIDVCFs(file)

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