find_contigsGapsTelos: get coordinates aggregated across kmers

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

get coordinates aggregated across kmers

Description

find_contigsGapsTelos find all positions with an exact match to any kmers and join them

Usage

find_contigsGapsTelos(
  dnass,
  teloKmers,
  minContigGapSize = 100,
  maxDistBtwTelo = 20,
  minTeloSize = 200,
  minTeloDens = 0.75,
  minChrSize = 0,
  maxDist2end = 10000,
  verbose = TRUE
)

Arguments

dnass	DNAStringSet containing the assembly fasta
teloKmers	character vector with the kmers in telomers
minContigGapSize	numeric, minimum size of a run of N's to be called a gap
maxDistBtwTelo	numeric, minimum distance between neighboring telomere kmers
minTeloSize	numeric, minimum size for telomere kmers cluster
minTeloDens	numeric (0-1), minimum density for telomere kmers
minChrSize	integer, minimum size of a scaffold to be included
maxDist2end	integer, maximum distance to the chromosome end for a telomere to be called at that arm.
verbose	logical, should updates be printed to the console?

Details

finds kmers and reduces overlapping intervals

Value

a granges object containing any sequences masked by the kmers

Examples

## Not run: 
# coming soon.

## End(Not run)

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