CreateOneColSBSMatrix

An in-memory VCF file annotated by the AddSeqContext and
AddTranscript functions. It must *not* contain indels and must *not*
contain DBS (double base substitutions), or triplet base substitutions
etc., even if encoded as neighboring SBS.

A <code><a rd-options="data.table" href="/link/data.table?package=ICAMS&version=2.0.8&to=data.table" data-mini-rdoc="data.table::data.table">data.table</a></code> which contains
transcript range and strand information. Please refer to
<code><a rd-options="" href="/link/TranscriptRanges?package=ICAMS&version=2.0.8" data-mini-rdoc="ICAMS::TranscriptRanges">TranscriptRanges</a></code> for more details.

trans.ranges

Usually the sample id, but defaults to "count".

sample.id

Create the matrix an SBS catalog for *one* sample from an in-memory VCF.

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')

CreateOneColSBSMatrix function

A <code><a rd-options='data.table' href='data.table'>data.table</a></code> which contains
transcript range and strand information. Please refer to
<code><a rd-options='' href='TranscriptRanges'>TranscriptRanges</a></code> for more details.

CreateOneColSBSMatrix: Create the matrix an SBS catalog for one sample from an in-memory VCF.

Description

Usage

Arguments

Value