TranscriptRanges

trans.ranges.GRCh37

trans.ranges.GRCh38

trans.ranges.GRCm38

Transcript ranges and strand information for a particular reference genome.

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')

TranscriptRanges function

A <code><a href="https://rdatatable.gitlab.io/data.table/reference/data.table.html">data.table</a></code> which contains transcript
 range and strand information for a particular reference genome.
 <code>colname</code>s are <code>chrom</code>, <code>start</code>, <code>end</code>, <code>strand</code>,
 <code>Ensembl.gene.ID</code>, <code>gene.symbol</code>. It uses one-based coordinates.
An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 19083 rows and 6 columns.
An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 19096 rows and 6 columns.
An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 20325 rows and 6 columns.

Format

Transcript ranges data — TranscriptRanges

A <code><a href='https://rdatatable.gitlab.io/data.table/reference/data.table.html'>data.table</a></code> which contains transcript
 range and strand information for a particular reference genome.
 <code>colname</code>s are <code>chrom</code>, <code>start</code>, <code>end</code>, <code>strand</code>,
 <code>Ensembl.gene.ID</code>, <code>gene.symbol</code>. It uses one-based coordinates.
An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 19083 rows and 6 columns.
An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 19096 rows and 6 columns.
An object of class <code>data.table</code> (inherits from <code>data.frame</code>) with 20325 rows and 6 columns.

TranscriptRanges: Transcript ranges data

Description

Usage

Arguments

Format

Details

Examples