loopsMake.mango reads in a data directory created by the
mango preprocessing pipeline and returns a loops object
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A string. The preprocessed data directory; Required
A character vector. Optional list of samples to read in
An integer value of the radius to merge anchors; default 500
Specificies 'all' or 'fdr' file format; default 'all'
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 being the default. Under the
default, all samples with the extension
.fdr.mango will be processed.
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
cut, or something similar.
A loops object where 'chr' is removed from the anchors.
# UPDATE THIS bd<- system.file('extdata', 'esc_jurkat', package='diffloopdata')
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