all.abundance: K-mer abundances

In ICAMS: In-Depth Characterization and Analysis of Mutational Signatures ('ICAMS')

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.

ICAMS documentation built on June 22, 2024, 6:47 p.m.