gpatterns.intervals_coverage: Get coverage of intervals in multiple tracks

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Get coverage of intervals in multiple tracks

Description

Get coverage of intervals in multiple tracks

Usage

gpatterns.intervals_coverage(
  tracks,
  intervals,
  iterator = NULL,
  file = NULL,
  intervals.set.out = NULL,
  pre_screen = TRUE,
  frag_cov = FALSE
)

Arguments

tracks	methylation tracks
intervals	genomic scope for which the function is applied
iterator	see iterator in gextract. if NULL iterator would be set to CpGs
file	save output to file (only in non tidy mode, would not filer by variance)
intervals.set.out	save output big intervals set (only in tidy mode, would not filter by variance)
pre_screen	screen for covered intervals before calculating the total coverage (for large intervals set)
frag_cov	use fragment coverage (if exists)

Value

intervals set with 'sum' column containing the total coverage (sum) in all the tracks

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