all.abundance {ICAMS} | R Documentation |
K-mer abundances
Description
An R list with one element each for
BSgenome.Hsapiens.1000genomes.hs37d5
,
BSgenome.Hsapiens.UCSC.hg38
and BSgenome.Mmusculus.UCSC.mm10
.
Each element is in turn a sub-list keyed by
exome
, transcript
,
and genome
. Each element of the sub list
is keyed by the number of rows in the catalog class (as a string, e.g.
"78"
, not 78
). The keys are:
78 (DBS78Catalog
), 96 (SBS96Catalog
), 136 (DBS136Catalog
),
144 (DBS144Catalog
), 192 (SBS192Catalog
),
and 1536 (SBS1536Catalog
). So, for example to get the exome
abundances for SBS96 catalogs for BSgenome.Hsapiens.UCSC.hg38
exomes
one would reference
all.abundance[["BSgenome.Hsapiens.UCSC.hg38"]][["exome"]][["96"]]
or all.abundance$BSgenome.Hsapiens.UCSC.hg38$exome$"96"
.
The value of the abundance is an integer vector with the K-mers
as names and each value being the count of that K-mer.
Usage
all.abundance
Format
See Description.
Examples
all.abundance$BSgenome.Hsapiens.UCSC.hg38$transcript$`144`
# AA AC AG AT CA CC ...
# 90769160 57156295 85738416 87552737 83479655 63267896 ...
# There are 90769160 AAs on the sense strands of transcripts in
# this genome.