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

In koustav-pal/HiCBlocks: Framework for Storing and Accessing Hi-C Data Through HDF Files

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

Description

Create_many_Bricks_from_mcool is a wrapper on Create_many_Bricks which creates the Brick data structure from an mcool file.

Usage

Create_many_Bricks_from_mcool(
    output_directory = NA,
    file_prefix = NA,
    mcool = NULL,
    resolution = NULL,
    experiment_name = NA,
    remove_existing = FALSE
)

Arguments

output_directory	Required A string specifying the location where the HDF files will be created.
file_prefix	Required A string specifying the prefix that is concatenated to the hdf files stored in the output_directory.
mcool	Required. Path to an mcool file.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
experiment_name	Optional. If provided, this will be the experiment name for the BrickContainer.
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)
out_dir <- file.path(tempdir(),"mcool_test_dir")
dir.create(path = out_dir)
curl_download(url = paste("https://data.4dnucleome.org/",
"files-processed/4DNFI7JNCNFB/",
"@download/4DNFI7JNCNFB.mcool", sep = ""),
destfile = file.path(out_dir,"H1-hESC-HiC-4DNFI7JNCNFB.mcool"))

mcool <- file.path(out_dir,"H1-hESC-HiC-4DNFI7JNCNFB.mcool")

Create_many_Bricks_from_mcool(output_directory = out_dir,
file_prefix = "Test",
mcool = mcool,
resolution = 50000,
experiment_name = "A random 4DN dataset")


## End(Not run)

koustav-pal/HiCBlocks documentation built on Oct. 29, 2022, 8:17 a.m.