loopsMake.mango: Read preprocessed ChIA-PET data from mango

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

loopsMake.mango reads in a data directory created by the mango preprocessing pipeline and returns a loops object

Usage

loopsMake.mango(beddir, samples = NA, mergegap = 500, ext = "all")

## S4 method for signature 'ANY'
loopsMake.mango(beddir, samples = NA, mergegap = 500,
  ext = "all")

Arguments

beddir	A string. The preprocessed data directory; Required
samples	A character vector. Optional list of samples to read in
mergegap	An integer value of the radius to merge anchors; default 500
ext	Specificies 'all' or 'fdr' file format; default 'all'

Details

This function reads in preprocessed ChIA-PET data produced by the mango preprocessing pipeline. The samples argument specifies which samples are read. If samples is not specified all samples will be read. The ext specifies which type of file to look for, either all or fdr, with all being the default. Under the default, all samples with the extension .fdr.mango will be processed. Finally, the FDR parameter (default = 1) specifies the minimum threshold for loops to be added to the greater loops object. Currently, we do not support importing the verbose output, so the verbose parameter when executing mango should be set to FALSE or the user will have ot parse the file before reading into diffloop using awk, cut, or something similar.

Value

A loops object where 'chr' is removed from the anchors.

Examples

# UPDATE THIS
bd<- system.file('extdata', 'esc_jurkat', package='diffloopdata')

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.