Brick_load_data_from_mcool: Load a NxN dimensional matrix into the Brick store from an...

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

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)

koustav-pal/HiCBricks documentation built on Oct. 25, 2022, 12:06 a.m.