gpatterns.extract: Extract pattern data

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Extract pattern data

Description

Extract pattern data

Usage

gpatterns.extract(
  ...,
  intervals,
  colnames = NULL,
  elements = c("fid", "ncpg", "n", "n0", "n1", "nx", "nc", "pat_meth"),
  add_bipolar_stats = FALSE,
  add_patterns = FALSE,
  add_cpg_content = FALSE,
  cpg_nhood = 500,
  add_coordinates = TRUE,
  tidy = TRUE,
  dsn = NULL,
  na.rm = TRUE
)

Arguments

...	tracks to extract
intervals	genomic scope to extract from intervals
colnames	names for the tracks
elements	elements to extract. default: fid,ncpg,n,n0,n1,nx,nc,pat_meth
add_bipolar_stats	add stats from bipolar model (if computed)
add_patterns	add patterns
add_cpg_content	add centered cpg content
cpg_nhood	scope for centered cpg content (in bp)
add_coordinates	add chrom,start,end for fragments
tidy	return tidy output
dsn	extract downsampled data
na.rm	remove rows with missing data

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