ReadTranscriptRanges

Read transcript ranges and strand information from a gff3 format file.
Use this one for the new, cut down gff3 file (2018 11 24)

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> 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')

ReadTranscriptRanges function

<dl><dt>file</dt>
<dd>Path to the file with the transcript information with 1-based
start end positions of genomic ranges.</dd></dl>

Arguments

Read transcript ranges and strand information from a gff3 format file.
Use this one for the new, cut down gff3 file (2018 11 24) — ReadTranscriptRanges

<dl>

<dt>file</dt>
<dd>Path to the file with the transcript information with 1-based
start end positions of genomic ranges.</dd>

</dl>

ReadTranscriptRanges: Read transcript ranges and strand information from a gff3 format file. Use this one for the new, cut down gff3 file (2018 11 24)

Description

Usage

Value

Arguments