Brick_return_region_position: Provides the overlapping position (within) from the bintable.

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

Provides the overlapping position (within) from the bintable.

Description

Brick_return_region_position takes as input a human-readable coordinate format of the form chr:start:end and outputs the overlapping bintable positions. This module does a "within" operation. So only bins which overlap completely with the region will be returned. This is not an iterable module, so the user has to make iterative calls to the module itself.

Usage

Brick_return_region_position(Brick, region, resolution = NA)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
region	Required. A character vector of length 1 specifying the region to overlap. It must take the form chr:start:end.
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 1 dimensional vector containing the position of the overlapping regions in the bintable associated the Brick store.

Design choice

This may seem to be a poor design choice at first glance, but I do not think this to be the case. By not being iterable, this function circumvents the problem of how to structure the data for the user. If one more element was accepted, the return object would have become a list, which increases the data structure complexity significantly for users who are just starting out with R. Therefore this problem is left for the users themselves to deal with.

Examples

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

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

Coordinate <- "chr2L:1:1000000"

Test_Run <- Brick_return_region_position(Brick = My_BrickContainer,
region = Coordinate, resolution = 100000)

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