loopsMake: Read preprocessed ChIA-PET data from dnaloop

Description Usage Arguments Details Value Examples

Description

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

Usage

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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

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# 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.