Brick_get_bintable: Returns the binning table associated to the Hi-C experiment.

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

Returns the binning table associated to the Hi-C experiment.

Description

Brick_get_bintable makes a call to Brick_get_ranges to retrieve the binning table of the associated Brick store. This is equivalent to passing the argument rangekey = "bintable" in Brick_get_ranges

Usage

Brick_get_bintable(Brick, chr = NA, resolution = NA)

Arguments

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

Value

Returns a GRanges object containing the binning table associated to the Brick store.

See Also

Brick_get_ranges

Examples

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

out_dir <- file.path(tempdir(), "list_get_bintable_test")
dir.create(out_dir)

My_BrickContainer <- Create_many_Bricks(BinTable = Bintable.path, 
    bin_delim = " ", output_directory = out_dir, file_prefix = "Test",
    experiment_name = "Vignette Test", resolution = 100000,
    remove_existing = TRUE)

Brick_get_bintable(Brick = My_BrickContainer, resolution = 100000)

koustav-pal/HiCLegos documentation built on Nov. 5, 2022, 5:49 p.m.