CreateOnePPMFromSBSVCF

One in-memory data frame of pure SBS mutations -- no DBS or 3+BS
mutations.

A <code>ref.genome</code> argument as described in
<code><a rd-options="" href="/link/ICAMS?package=ICAMS&version=2.0.7" data-mini-rdoc="ICAMS::ICAMS">ICAMS</a></code>.

ref.genome

The number of preceding and following bases to be
extracted around the mutated position from <code>ref.genome</code>.

seq.context.width

Create position probability matrix (PPM) for *one* sample from
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>. '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')

CreateOnePPMFromSBSVCF function

A <code>ref.genome</code> argument as described in
<code><a rd-options='' href='ICAMS'>ICAMS</a></code>.

CreateOnePPMFromSBSVCF: Create position probability matrix (PPM) for one sample from a Variant Call Format (VCF) file.

Description

Usage

Arguments

Value