all.abundance

<p>An R list with one element each for 
<code>BSgenome.Hsapiens.1000genomes.hs37d5</code>, 
<code>BSgenome.Hsapiens.UCSC.hg38</code> and <code>BSgenome.Mmusculus.UCSC.mm10</code>.
Each element is in turn a sub-list keyed by 
<code>exome</code>, <code>transcript</code>, 
and <code>genome</code>. Each element of the sub list
is keyed by the number of rows in the catalog class (as a string, e.g. 
<code>"78"</code>, not <code>78</code>). The keys are:
78 (<code>DBS78Catalog</code>), 96 (<code>SBS96Catalog</code>), 136 (<code>DBS136Catalog</code>),
144 (<code>DBS144Catalog</code>), 192 (<code>SBS192Catalog</code>),
 and 1536 (<code>SBS1536Catalog</code>). So, for example to get the exome
 abundances for SBS96 catalogs for <code>BSgenome.Hsapiens.UCSC.hg38</code> exomes
 one would reference 
 <code>all.abundance[["BSgenome.Hsapiens.UCSC.hg38"]][["exome"]]["96"]</code> 
 or <code>all.abundance$BSgenome.Hsapiens.UCSC.hg38$exome$"96"</code>.
 The value of the abundance is an integer vector with the K-mers
 as names and each value being the count of that K-mer.</p>

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>. '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.

all.abundance: K-mer abundances.

Description

Usage

Arguments

Format

Examples