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

View source: R/Brick_functions.R

Brick_get_bintableR Documentation

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.