cooler_methods: Methods for manipulating cooler files
In hansenlab/bnbc: Bandwise normalization and batch correction of Hi-C data

Description Usage Arguments Details Value See Also

These are a set of methods for working with data in cooler file format.

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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 `GRanges` object, can be output from `getChrIdx`.
`work.dir`	Directory for saving temporary files.
`exp.name`	The name of the experiment, will be appended all output file names.
`coldata`	A `data.frame` or `DataFrame` of metadata for the `ContactGroup` object.
`cg`	A `ContactGroup` object.
`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

hansenlab/bnbc documentation built on Dec. 23, 2020, 12:31 a.m.