GetStrandedKmerCounts: Generate stranded k-mer abundance from a given genome and...

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

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

Description

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

Usage

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

Arguments

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.

Value

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

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