R: Create the entire HDF5 structure and load the bintable from a...

CreateBrick_from_mcool {HiCBricks}

R Documentation

Create the entire HDF5 structure and load the bintable from a mcool file

Description

CreateBrick_from_mcool is a wrapper on CreateBrick which creates the Brick data structure from an mcool file.

Usage

CreateBrick_from_mcool(Brick, mcool, binsize = NULL, chrs = NULL,
    remove.existing = FALSE)

Arguments

`Brick`	Required. A string specifying the path to the Brick store created with CreateBrick.
`mcool`	Required. Path to an mcool file.
`binsize`	Optional. The binsize to select from an mcool file.
`chrs`	Optional. If provided will only create a Brick for these chromosomes (both cis & trans).
`remove.existing`	Optional. Default FALSE. If TRUE, will remove the HDF file with the same name and create a new one. By default, it will not replace existing files.

Details

mcool are a standard 4D nucleome data structure for Hi-C data. Read more about the 4D nucleome project here.

Value

This function will generate the target Brick file. Upon completion, the function will provide the path to the created/tracked HDF file.

Examples


## Not run: 
require(curl)
curl_download(url = paste("https://data.4dnucleome.org/"
"files-processed/4DNFI7JNCNFB/"
"@download/4DNFI7JNCNFB.mcool",sep = ""),
destfile = file.path(temp.dir(),"H1-hESC-HiC-4DNFI7JNCNFB.mcool"))

Output.brick <- file.path(tempdir(), 
"H1-hESC-HiC-4DNFI7JNCNFB-10000-ICE-normalised-chr1.brick")
mcool <- file.path(temp.dir(),"H1-hESC-HiC-4DNFI7JNCNFB.mcool")

CreateBrick_from_mcool(Brick = Output.brick,
mcool = mcool,
binsize = 10000,
chrs = "chr1")


## End(Not run)

[Package HiCBricks version 1.2.0 Index]