Canonicalize1DEL

The deleted sequence plus ample surrounding
sequence on each side (at least as long as <code>del.seq</code>).

context

The deleted sequence in <code>context</code>.

del.seq

The position of <code>del.sequence</code> in <code>context</code>.

If &gt; 0 cat information how the computation is carried out.

trace

Given a deletion and its sequence context, categorize it.

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.

Canonicalize1DEL: Given a deletion and its sequence context, categorize it.

Description

Usage

Arguments

Value