loopsMake: Read preprocessed ChIA-PET data from dnaloop
In diffloop: Identifying differential DNA loops from chromatin topology data

Description Usage Arguments Details Value Examples

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

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

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

`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'

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.

A loops object

# 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')