gpatterns.intervs_to_pat_space: Generate pattern space for specific genomic loci

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Generate pattern space for specific genomic loci

Description

Generate pattern space for specific genomic loci

Usage

gpatterns.intervs_to_pat_space(
  tracks,
  intervals,
  pat_len,
  adjacent = TRUE,
  add_rest = FALSE,
  min_cov = 1,
  max_span = 500,
  expand_intervals = FALSE,
  nchunks = getOption("gpatterns.parallel.thread_num"),
  parallel = getOption("gpatterns.parallel"),
  verbose = FALSE
)

Arguments

tracks	tracks
intervals	genomic loci to cover (chrom,start,end), with an optional field 'fid'.
pat_len	pattern length
adjacent	generate patterns that do not skip a CpG
add_rest	add rest of the genome (using gpatterns.tracks_to_pat_space)
min_cov	if adjacent: minimal pattern coverage for interval. else - minimal CpG coverage
max_span	maximum span to look for CpGs
expand_intervals	expand intervals by max_span when intervals are single CpG loci
nchunks	override global gpatterns.parallel.thread_num definition
parallel	override global gpatterns.parallel definition
verbose	print additional progress messages

tanaylab/gpatterns documentation built on May 15, 2023, 6:23 p.m.