GetCustomKmerCounts: Generate custom k-mer abundance from a given reference genome

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

Description

Generate custom k-mer abundance from a given reference genome

Usage

GetCustomKmerCounts(k, ref.genome, custom.ranges, filter.path, verbose = FALSE)

Arguments

k	Length of k-mers (k>=2)
ref.genome	A ref.genome argument as described in ICAMS.
filter.path	If given, homopolymers will be masked from genome(sequence). Only simple repeat masking is accepted now.
verbose	If TRUE generate progress messages.
custom.range	A keyed data table which has custom ranges information. It has three columns: chrom, start and end. It should use one-based coordinate system. You can use the internal function in this package ICAMS:::ReadBedRanges to read a BED file in 0-based coordinates and convert it to 1-based coordinates.

Value

Matrix of the counts of custom k-mer across the ref.genome

ICAMS documentation built on April 3, 2021, 5:07 p.m.