ICAMS: GetStrandedKmerCounts – R documentation

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GetStrandedKmerCounts

Generate stranded k-mer abundance from a given genome and gene annotation file

Generate stranded k-mer abundance from a given genome and gene annotation file

GetStrandedKmerCounts(
  k,
  ref.genome,
  stranded.ranges,
  filter.path,
  verbose = FALSE
)

`k`	Length of k-mers (k>=2)
`ref.genome`	A `ref.genome` argument as described in `ICAMS`.
`stranded.ranges`	A keyed data table which has stranded ranges information. It has four columns: chrom, start, end and strand. It should use one-based coordinate system.
`filter.path`	If given, homopolymers will be masked from genome(sequence). Only simple repeat masking is accepted now.
`verbose`	If `TRUE` generate progress messages.

Matrix of the counts of each stranded k-mer across the ref.genome

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

v2.3.10

GPL-3 | file LICENSE

Authors

Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu, Yang Wu

Initial release