readEpibed: Read in and decode the RLE representation of the epibed...

In trichelab/biscuitEater: Convenience Functions for Biscuit

Read in and decode the RLE representation of the epibed format out of biscuit epiread

Description

Read in and decode the RLE representation of the epibed format out of biscuit epiread

Usage

readEpibed(
  epibed,
  genome = NULL,
  chr = NULL,
  start = 1,
  end = 2^28,
  fragment_level = TRUE
)

Arguments

epibed	The path to the epibed file (must be bgzip and tabix indexed)
genome	What genome did this come from (e.g. 'hg19') (default: NULL)
chr	Which chromosome to retrieve (default: NULL)
start	The starting position for a region of interest (default: 1)
end	The end position for a region of interest (default: 2^28)
fragment_level	Whether to collapse reads to the fragment level (default: TRUE)

Value

A GRanges object

Examples

epibed.nome <- system.file("extdata", "hct116.nome.epibed.gz", package="biscuiteer")
epibed.bsseq <- system.file("extdata", "hct116.bsseq.epibed.gz", package="biscuiteer")

epibed.nome.gr <- readEpibed(epibed = epibed.nome, genome = "hg19", chr = "chr1")
epibed.bsseq.gr <- readEpibed(epibed = epibed.bsseq, genome = "hg19", chr = "chr1")

trichelab/biscuitEater documentation built on March 2, 2024, 6:57 p.m.