Brick_load_data_from_mcool {HiCBricks} | R Documentation

## Load a NxN dimensional matrix into the Brick store from an mcool file.

### Description

Read an mcool contact matrix coming out of 4D nucleome projects into a Brick store.

### Usage

    Brick_load_data_from_mcool(
        Brick,
        mcool,
        resolution = NULL,
        matrix_chunk = 2000,
        cooler_read_limit = 1e+07,
        remove_prior = FALSE,
        norm_factor = "Iterative-Correction"
    )

### Arguments

`Brick` | Required. A string specifying the path to the Brick store created with Create_many_Brick.
`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
`matrix_chunk` | Optional. Default 2000. The nxn matrix square to fill per iteration in a mcool file.
`cooler_read_limit` | Optional. Default 10000000. cooler_read_limit sets the upper limit for the number of records per matrix chunk. If the number of records per chunk is higher than this value, the matrix_chunk value will be re-evaluated dynamically.
`remove_prior` | Optional. Default FALSE If a matrix was loaded before, it will not be replaced. Use remove_prior to override and replace the existing matrix.
`norm_factor` | Optional. Default "Iterative-Correction". The normalization factor to use for normalization from an mcool file. norm_factor currently accepts one of "Iterative-Correction", "Knight-Ruitz", "Vanilla-coverage", "Vanilla-coverage-square-root" and NULL. If NULL, the function will load only counts from the mcool file.

### Value

Returns TRUE if all went well.

### See Also

`Create_many_Bricks_from_mcool` to create matrix from an mcool file, `Brick_list_mcool_resolutions` to list available resolutions in an mcool file, `Brick_list_mcool_normalisations` to list available normalisation factors in the mcool file.

### Examples

    ## Not run:

    require(curl)
    out_dir <- file.path(tempdir(),"mcool_load_test")
    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")

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

    Brick_load_data_from_mcool(Brick = My_BrickContainer, mcool = mcool,
    resolution = 50000, matrix_chunk = 2000, remove_prior = TRUE,
    norm_factor = "Iterative-Correction")

    ## End(Not run)

[Package HiCBricks version 1.10.0 Index]