CatalogRowOrder

catalog.row.order

This data is designed for those
who need to create their own catalogs from formats not
supported by this package. The rownames denote the mutation
types. For example, for SBS96 catalogs, the rowname
 AGAT represents a mutation from AGA &gt; ATA.

datasets

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> and
"Characterization of colibactin-associated mutational signature in an
Asian oral squamous cell carcinoma and in other mucosal tumor types",
Genome Research 2020 <doi:10.1101/gr.255620.119>.
'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" (i.e.
representation as mutations per megabase) mutational spectra or signatures.

Steve Rozen

ICAMS

In-Depth Characterization and Analysis of Mutational Signatures
('ICAMS')

CatalogRowOrder function

A list of character vectors indicating the standard
 orders of row names in catalogs.
An object of class <code>list</code> of length 8.

Format

See <a href="https://github.com/steverozen/ICAMS/blob/master/data-raw/PCAWG7_indel_classification_2021_09_03.xlsx">https://github.com/steverozen/ICAMS/blob/master/data-raw/PCAWG7_indel_classification_2021_09_03.xlsx</a>
for additional information on ID (small insertion and deletion) mutation
classification.
See the documentation for <code>Canonicalize1Del</code> which first handles
deletions in homopolymers, then handles deletions in simple repeats with
longer repeat units, (e.g. <code>CACACACA</code>, see
<code>FindMaxRepeatDel</code>), and if the deletion is not in a simple
repeat, looks for microhomology (see <code>FindDelMH</code>).
See the code for unexported function <code>CanonicalizeID</code>
and the functions it calls for handling of insertions.

ID classification

Standard order of row names in a catalog — CatalogRowOrder

See <a href='https://github.com/steverozen/ICAMS/blob/master/data-raw/PCAWG7_indel_classification_2021_09_03.xlsx'>https://github.com/steverozen/ICAMS/blob/master/data-raw/PCAWG7_indel_classification_2021_09_03.xlsx</a>
for additional information on ID (small insertion and deletion) mutation
classification.
See the documentation for <code>Canonicalize1Del</code> which first handles
deletions in homopolymers, then handles deletions in simple repeats with
longer repeat units, (e.g. <code>CACACACA</code>, see
<code>FindMaxRepeatDel</code>), and if the deletion is not in a simple
repeat, looks for microhomology (see <code>FindDelMH</code>).
See the code for unexported function <code>CanonicalizeID</code>
and the functions it calls for handling of insertions.

CatalogRowOrder: Standard order of row names in a catalog

Description

Usage

Arguments

Format

ID classification

Examples