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

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

Generate custom k-mer abundance from a given reference genome

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.
custom.ranges	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.
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 custom k-mer across the ref.genome

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