Brick_add_ranges: Store a ranges object in the Brick store.

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

Store a ranges object in the Brick store.

Description

Brick_add_ranges loads a GRanges object into the Brick store.

Usage

Brick_add_ranges(
    Brick,
    ranges,
    rangekey,
    resolution = NA,
    all_resolutions = FALSE,
    num_cpus = 1
)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
ranges	Required. An object of class ranges specifying the ranges to store in the Brick.
rangekey	Required. The name to use for the ranges within the Brick store.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
all_resolutions	Optional. Default FALSE If resolution is not defined and all_resolutions is TRUE, the resolution parameter will be ignored and the function is executed on all files listed in the Brick container
num_cpus	Optional. Default 1 When an object of class BrickContainer is provided, num_cpus defines the maximum number of parallel jobs that will be run.

Details

With this function it is possible to associate other ranges objects with the Brick store. If metadata columns are present, the are also loaded into the Brick store. Although not explicitly asked for, the metadata columns should not be of type list as this may create complications down the line. We ask for ranges objects, so if the same ranges object is later retrieved two additional columns will be present. These are the strand and width columns that are obtained when a ranges is converted into a data.frame. Users can ignore these columns.

Value

Returns TRUE if completed successfully.

Examples

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

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

Chrom <- c("chrS","chrS","chrS","chrS","chrS")
Start <- c(10000,20000,40000,50000,60000)
End <- c(10001,20001,40001,50001,60001)
Test_ranges <- Brick_make_ranges(chrom = Chrom, start = Start, end = End)
Brick_add_ranges(Brick = My_BrickContainer, ranges = Test_ranges,
rangekey = "test_ranges", all_resolutions = TRUE)

koustav-pal/HiCBricks documentation built on Oct. 25, 2022, 12:06 a.m.