loopsMake: Read preprocessed ChIA-PET data from dnaloop

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

Description

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

Usage

loopsMake(beddir, samples = NA, mergegap = 0, type = "all")

## S4 method for signature 'ANY'
loopsMake(beddir, samples = NA, mergegap = 0,
  type = "all")

Arguments

beddir	A string. The preprocessed data directory
samples	A character vector. Optional list of samples to read in
mergegap	An integer value of the radius to merge anchors; default 0
type	Specificies 'intra', 'inter', or 'all' looping. Default 'all'

Details

This function reads in preprocessed ChIA-PET data produced by the dnaloop preprocessing pipeline. The samples argument specifies which samples are read. If samples is not specified all samples will be read. The type option restricts loops whether they are on the same 'intra' or different 'inter' chormosome. Default is 'all'.

IMPORTANT: Assumes the delimiter is a space, not a tab on the files.

Value

A loops object

Examples

# Reading in all samples, no mergegap, all loops
bd<- system.file('extdata', 'esc_jurkat', package='diffloopdata')
# loops <- loopsMake(bd) #standard call

# Reading in a subset of samples, 1kb mergegap, only intrachromosomal
# looping
samples <- c('naive_esc_1', 'naive_esc_2')
# naive.intra <- loopsMake(bd, samples, 1000, 'inter')

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