loopsMake {diffloop} | R Documentation |
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')