WriteCatalogIndelSigPro

A catalog as defined in <code><a rd-options="" href="/link/ICAMS?package=ICAMS&version=2.1.2" data-mini-rdoc="ICAMS::ICAMS">ICAMS</a></code>;
see also <code><a rd-options="" href="/link/as.catalog?package=ICAMS&version=2.1.2" data-mini-rdoc="ICAMS::as.catalog">as.catalog</a></code>.

catalog

The path to the file to be created.

file

If TRUE, do additional checks on the input, and stop if the
checks fail.

strict

Write Indel Catalogs in SigProExtractor format to a csv 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>. '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')

WriteCatalogIndelSigPro function

A catalog as defined in <code><a rd-options='' href='ICAMS'>ICAMS</a></code>;
see also <code><a rd-options='' href='as.catalog'>as.catalog</a></code>.

WriteCatalogIndelSigPro: Write Indel Catalogs in SigProExtractor format.

Description

Usage

Arguments