Create_many_Bricks_from_mcool {HiCBricks} | R Documentation

## 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)

[Package HiCBricks version 1.10.0 Index]