find_kmers: Generic internal functions used by genespace

In jtlovell/gscTools: Genome exploration R tools

Generic internal functions used by genespace

Description

find_kmers Convenience functions for gscTools, not meant to be called directly by the user. Little documentation support provided, use at your own risk.

find_manyKmers Finds exact DNA-DNA matches and aggregates across all kmers in the kmer DNAstring

find_runsOfNs Exact string matching of Ns to a DNAStringSet to find the position of gaps between contigs

Usage

find_manyKmers(dnass, kmers, nCores = 1)

find_runsOfNs(dnass, minRunLength)

Arguments

dnass	DNAStringSet
kmers	DNAStringSet with kmers to find
nCores	integer, then number of cores to use
bed	data.table or data.frame with at least chr, start, end columns
seqInfo	seqInfo ranges extracted from dnass
gr	granges object
existingGr	existing granges to mask with
newGr	new granges to mask
x	single-value parameter, string, integer, numeric, list, vector
...	additional arguments passed on If called, find_kmers returns its own arguments.

jtlovell/gscTools documentation built on March 16, 2023, 10:24 p.m.