CreateOneColIDMatrix

An in-memory VCF as a data.frame annotated by the
 <code><a rd-options="" href="/link/AddAndCheckSequenceID?package=ICAMS&version=2.0.7" data-mini-rdoc="ICAMS::AddAndCheckSequenceID">AddAndCheckSequenceID</a></code> function. It must only
 contain indels and must not contain SBSs
 (single base substitutions), DBSs, or triplet
 base substitutions, etc.
One design decision for variant callers is the representation of "complex
 indels", e.g. mutations e.g. CAT &gt; GC. Some callers represent this as C&gt;G,
 A&gt;C, and T&gt;_. Others might represent it as CAT &gt; CG. Multiple issues can
 arise. In PCAWG, overlapping indel/SBS calls from different callers were
 included in the indel VCFs.

ID.vcf

An in-memory VCF as a data frame. Because we have to work with
some PCAWG data, we will look for neighboring indels and indels adjoining
SBS. That means this functions takes an SBS VCF and an ID VCF from the same
sample.

SBS.vcf

Create one column of the matrix for an indel catalog from *one* 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')

CreateOneColIDMatrix function

An in-memory VCF as a data.frame annotated by the
 <code><a rd-options='' href='AddAndCheckSequenceID'>AddAndCheckSequenceID</a></code> function. It must only
 contain indels and must not contain SBSs
 (single base substitutions), DBSs, or triplet
 base substitutions, etc.
One design decision for variant callers is the representation of "complex
 indels", e.g. mutations e.g. CAT &gt; GC. Some callers represent this as C&gt;G,
 A&gt;C, and T&gt;_. Others might represent it as CAT &gt; CG. Multiple issues can
 arise. In PCAWG, overlapping indel/SBS calls from different callers were
 included in the indel VCFs.

CreateOneColIDMatrix: Create one column of the matrix for an indel catalog from one in-memory VCF.

Description

Usage

Arguments

Value