Brick_get_chrominfo: Get the chrominfo for the Hi-C experiment.

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

Get the chrominfo for the Hi-C experiment.

Description

Brick_get_chrominfo fetches the associated chrominfo table for the Brick it is associated to.

Usage

Brick_get_chrominfo(Brick, resolution = NA)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed

Value

A three column data.frame containing chromosomes, nrows and length.

chromosomes corresponds to all chromosomes in the provided bintable.

nrows corresponds to the number of entries in the bintable or dimension for that chromosome in a Hi-C matrix.

Length is the total bp length of the same chromosome (max value for that chromosome in the bintable).

Examples

Bintable_path <- system.file(file.path("extdata", "Bintable_100kb.bins"), 
package = "HiCBricks")

out_dir <- file.path(tempdir(), "HiCBricks_chrominfo_test")

dir.create(out_dir)

My_BrickContainer <- Create_many_Bricks(BinTable = Bintable_path, 
bin_delim=" ", remove_existing=TRUE, output_directory = out_dir, 
file_prefix = "HiCBricks_vignette_test", resolution = 100000,
experiment_name = "HiCBricks vignette test")

Brick_get_chrominfo(Brick = My_BrickContainer, resolution = 100000)

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