| 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')