gpatterns.create_patterns_track: Creates patterns attributes of track

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Creates patterns attributes of track

Description

Creates patterns attributes of track

Usage

gpatterns.create_patterns_track(
  track,
  description,
  pat_space,
  patterns_tab = NULL,
  add_read_id = TRUE,
  noise_threshold = 0.2,
  overwrite = TRUE,
  canonize = FALSE,
  add_biploar_stats = FALSE,
  ...
)

Arguments

track	track name
description	a character string description
pat_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
patterns_tab	table with patterns (output of gpatterns.tidy_cpgs_to_pats) needs to have the following fields: fid,pattern. If NULL it would be generated automatically.
add_read_id	save the read_id together with the patterns
noise_threshold	threshold to consider pattern as 'noise'
overwrite	overwrite existing tracks
canonize	convert to canonic form (see: gintervals.canonic). warning: may lose data
add_biploar_stats	run mixture model and add bipolaritly stats. (warning: heavy computation)
...	additional parameters for gpatterns.calc_bipolarity

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