AddAndCheckSequenceID

A data frame storing mutation records of a VCF file
 containing only insertions and deletions. This function expects that
 there is a "context base" to the left, for example REF = ACG, ALT = A
(deletion of CG) or REF = A, ALT = ACC (insertion of CC).

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

If &gt; 0, if there are mismatches to references, print
out the mismatched rows and continue. Otherwise <code>stop</code>.

flag.mismatches

Add sequence context to a data frame with ID (insertion/deletion) mutation records,
 and confirm that they match the given reference genome.

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')

AddAndCheckSequenceID function

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

Add sequence context to a data frame with ID (insertion/deletion) mutation records,
 and confirm that they match the given reference genome. — AddAndCheckSequenceID

AddAndCheckSequenceID: Add sequence context to a data frame with ID (insertion/deletion) mutation records, and confirm that they match the given reference genome.

Description

Usage

Arguments

Value