loopsMake.mango {diffloop} | R Documentation

## Read preprocessed ChIA-PET data from mango

### 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')

[Package diffloop version 1.20.0 Index]