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.

See Also

Brick_load_data_from_mcool to load data from the mcool to a Brick store.

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]