loopsMake {diffloop} | R Documentation

## Read preprocessed ChIA-PET data from dnaloop

### 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')

[Package diffloop version 1.8.0 Index]