diffloop (version 1.0.2)

loopsMake: Read preprocessed ChiA-PET 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")
## S3 method for class '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'

Value

• A loops object

Details

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

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, 'intra')