ReadVCF

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

file

Name of the variant caller that produces the VCF, can
be either <code>strelka</code>, <code>mutect</code> or <code>freebayes</code>. This
information is needed to calculate the VAFs (variant allele frequencies).
If <code>NULL</code>(default), then VAF and read depth information will not be
added to the original VCF.

variant.caller

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

Optional. Only applicable to Mutect VCF. Name
of the column in Mutect 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=2.2.4" data-mini-rdoc="ICAMS::GetMutectVAF">GetMutectVAF</a></code> for
more details.

tumor.col.name

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

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.

Steve Rozen

ICAMS

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

ReadVCF function

Optional. Only applicable to Mutect VCF. Name
of the column in Mutect 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.

ReadVCF: Read in the data lines of a Variant Call Format (VCF) file

Description

Usage

Arguments

Value