ReadStrelkaSBSVCFs

Character vector of file paths to the VCF files.

files

Character vector of names of the VCF files. The order
of names in <code>names.of.VCFs</code> should match the order of VCF file paths
in <code>files</code>. If <code>NULL</code>(default), this function will remove all of
the path up to and including the last path separator (if any) and file
paths without extensions (and the leading dot) will be used as the names of
the VCF files.

names.of.VCFs

Read Strelka SBS (single base substitutions) VCF files.

internal

Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<doi:10.1101/gr.230219.117>. 'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based" catalogs
of mutational spectra or signatures.

ReadStrelkaSBSVCFs: Read Strelka SBS (single base substitutions) VCF files.

Description

Usage

Arguments

Value