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

Description Usage Arguments Details Value See Also Examples

These are a set of methods for working with data in cooler file format. At present this assumes there is one sample's data at one resolution per cooler file, for all observations from one sample.

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getGenomeIdx(file, step)
getChrCGFromCools(bin.ixns, files, chr, colData)
cg2bedgraph2(cg, out.dir)

`file`	The name of a cooler file.
`step`	The resolution of the data inside the cooler file.
`bin.ixns`	A list that contains a list of interactions and the bins involved; output of `getGenomeIdx`.
`files`	A vector of cooler file names.
`chr`	The target chromosome to be read.
`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.

These methods allow for the normalization of cooler files. Users must first generate an index of the genome represented in all cooler files (it is assumed the same loci pair's interactions are observed in all samples), which allows for subsequent efficient I/O operations. getGenomeIdx generates this index. The index can then be used to pull data for one chromosome for all cooler files using getChrCGFromCools. 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.

For getGenomeIdx, a list that contains a set of all interactions, as well as a listing of all bins present in the cooler file cool.fh. For getChrCGFromCools, a ContactGroup object. There is nothing returned by cg2bedgraph2.

ContactGroup

coolerDir <- system.file("cooler", package = "bnbc")
cools <- list.files(coolerDir, pattern="cool$", full.names=TRUE)

step <- 4e4

bin.ixns.list <- bnbc:::getGenomeIdx(cools[1], step)
bin.ixns <- bin.ixns.list$bin.ixns

data(cgEx)
cool.cg <- bnbc:::getChrCGFromCools(bin.ixns,
                                    files = cools,
                                    chr = "chr22",
                                    colData = colData(cgEx)[1:2,])
all.equal(contacts(cgEx)[[1]], contacts(cool.cg)[[1]])