Brick_get_ranges {HiCBricks} | R Documentation

## Fetch the ranges associated to a rangekey or chromosome.

### 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)

[Package HiCBricks version 1.4.0 Index]