Brick_get_ranges: Fetch the ranges associated to a rangekey or chromosome.

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

Description

Brick_get_ranges will get a ranges object if present in the Brick store and return a GRanges object.

Usage

Brick_get_ranges(Brick = NA, chr = NA, rangekey = 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.
rangekey	Required. A string specifying the name of the ranges.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed

Details

If a rangekey is present, the ranges will be retrieve and a GRanges constructed. Metadata columns will also be added. If these are rangekeys other than "Bintable", and had been added using Brick_add_ranges the width and Strand columns may appear as metadata columns. These will most likely be artifacts from converting the original ranges object to a data.frame.

Value

Returns a GRanges object with the associated metadata columns that may have been present in the Ranges object.

Examples

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

out_dir <- file.path(tempdir(), "list_get_ranges_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_ranges(Brick = My_BrickContainer, chr = "chr2L", 
rangekey = "Bintable", resolution = 100000)

HiCBricks documentation built on Nov. 8, 2020, 7:45 p.m.