ReadMutectVCF

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

file

Name of the column in VCF which contains the tumor
sample information. It must have quotation marks. If
<code>tumor.col.name</code> is equal to <code>NA</code>(default), this function will
use the 10th column to calculate VAFs. See <code><a rd-options="" href="/link/GetMutectVAF?package=ICAMS&version=2.0.10" data-mini-rdoc="ICAMS::GetMutectVAF">GetMutectVAF</a></code> for
more details.

tumor.col.name

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

Read in the data lines of a Variant Call Format (VCF) file created by
 Mutect

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.

Steve Rozen

ICAMS

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

ReadMutectVCF function

Name of the column in VCF which contains the tumor
sample information. It must have quotation marks. If
<code>tumor.col.name</code> is equal to <code>NA</code>(default), this function will
use the 10th column to calculate VAFs. See <code><a rd-options='' href='GetMutectVAF'>GetMutectVAF</a></code> for
more details.

ReadMutectVCF: Read in the data lines of a Variant Call Format (VCF) file created by Mutect

Description

Usage

Arguments

Value