gpatterns.tidy_cpgs_to_pats: Extracts patterns given pattern space

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Extracts patterns given pattern space

Description

Extracts patterns given pattern space

Usage

gpatterns.tidy_cpgs_to_pats(
  track,
  pattern_space = NULL,
  pattern_space_file = NULL,
  max_missing = Inf,
  min_cov = 1,
  by_coord_bin = TRUE,
  parallel = getOption("gpatterns.parallel"),
  ...
)

Arguments

track	name of track
pattern_space	pattern space data frame (output of gpatterns.tracks_to_pat_space or gpatterns.intervs_to_pat_space) needs to have the following fields: chrom,start,end,fid
pattern_space_file	file that holds the pattern space
max_missing	maximal number of missing data ('*') in pattern
min_cov	minimal pattern coverage
by_coord_bin	execute separatly for each coordinates bin (for tracks that do not fit into memory)
...	additional parameters to gpatterns.apply_tidy_cpgs

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