all.abundance

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.

datasets

ICAMS

all.abundance function

Format

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.

all.abundance: K-mer abundances

Description

Usage

Arguments

Format

Examples