find_kmers: Generic internal functions used by genespace

In jtlovell/GENESPACE: Synteny- and orthology-constrained comparative genomics

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_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

find_telomeres find_telomeres

Usage

find_manyKmers(dnass, kmers, nCores = 1)

find_fewKmers(dnass, kmers, nCores = 1, ...)

find_runsOfNs(dnass, minRunLength)

find_telomeres(
  dnass,
  kmers,
  maxDistBtwTelo = 20,
  minTeloSize = 200,
  minTeloDens = 0.75,
  maxDist2end = 10000,
  nCores = 1
)

Arguments

dnass	DNAStringSet
kmers	DNAStringSet with kmers to find
nCores	integer, then number of cores to use
...	additional arguments passed to vmatchpattern If called, find_kmers returns its own arguments.
minRunLength	numeric, the minimum size for a kmer run to be counted
maxDistBtwTelo	numeric, maximum distance between two telomere kmers for the telomere run to be considered a single run
minTeloSize	numeric, the minimum number of bases for a telomere run to be counted
minTeloDens	numeric [0-1], the minimum density of telomere kmers in the run
maxDist2end	numeric, the maximum distance to a chromosome end for a telomere to be called terminal (and not interstitial)

jtlovell/GENESPACE documentation built on Jan. 25, 2025, 6:39 a.m.