Generate stranded k-mer abundance from a given genome and gene annotation file
GetStrandedKmerCounts(k, ref.genome, stranded.ranges, filter.path,
verbose = FALSE)
Length of k-mers (k>=2)
A ref.genome
argument as described in
ICAMS
.
A keyed data table which has stranded ranges information. It has four columns: chrom, start, end and strand.
If given, homopolymers will be masked from genome(sequence). Only simple repeat masking is accepted now.
If TRUE
generate progress messages.
Matrix of the counts of each stranded k-mer across the ref.genome