ReadStrelkaSBSVCF

The name/path of the VCF file, or a complete URL.

file

Name of the VCF file. If <code>NULL</code>(default), this
function will remove all of the path up to and including the last path
separator (if any) in <code>file</code> and file path without extensions (and the
leading dot) will be used as the name of the VCF file.

name.of.VCF

Logical. Whether to suppress
warning messages showing information about the discarded variants. Default
is TRUE.

suppress.discarded.variants.warnings

Read in the data lines of an SBS VCF created by Strelka version 1

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> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <doi:10.1101/gr.255620.119>.
'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.

ReadStrelkaSBSVCF: Read in the data lines of an SBS VCF created by Strelka version 1

Description

Usage

Arguments

Value