Description Usage Arguments Details Value See Also
These are a set of methods for working with data in cooler file format.
1 2 3 | getChrIdx(chr.length, step)
getChrCGFromCools(files, chr, step, index.gr, work.dir, exp.name, coldata)
cg2bedgraph2(cg, out.dir, prefix)
|
chr.length |
The length of a chromosome. |
step |
The resolution of the data inside the cooler file. |
files |
A vector of cooler file names. |
chr |
The target chromosome to be read. |
index.gr |
A |
work.dir |
Directory for saving temporary files. |
exp.name |
The name of the experiment, will be appended all output file names. |
coldata |
A |
cg |
A |
out.dir |
A directory in which individual bedgraph2 (BG2) files are to be written. |
prefix |
A prefix for all output files; e.g. "treatment_study_". |
These methods allow for the normalization of cooler files. Users must
create their own index, for which we provide getChrIdx
, which
is an input into getChrCGFromCools
, which uses HiCBricks to
access the cooler files, and returns a ContactGroup
object. Users can then follow the standard pipeline, and save their
data in bedgraph2 (BG2) format using cg2bedgraph2
. cooler
provides a tool to convert this format to cooler and users are
encouraged to make use of this tool. Note that HiCBricks expects
multiple resolutions in the cooler file.
For getChrIdx
a GRanges
object with coordinates
for each bin. For getChrCGFromCools
, a
ContactGroup
object. There is nothing returned by
cg2bedgraph2
.
ContactGroup
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