Brick_matrix_maxdist: Get the maximum loaded distance from the diagonal of any...

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

Get the maximum loaded distance from the diagonal of any matrix.

Description

If values beyond a certain distance were not loaded in the matrix, this distance parameter is useful. This package by default will check this param to make sure that it is not returning non-existent data.

Usage

Brick_matrix_maxdist(Brick, chr1, chr2, resolution = NA)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
chr1	Required. A character vector of length 1 specifying the chromosome corresponding to the rows of the matrix
chr2	Required. A character vector of length 1 specifying the chromosome corresponding to the columns of the matrix
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed

Details

Brick_matrix_maxdist will return this parameter.

Value

Returns an integer vector of length 1, specifying the maximum distance loaded for that matrix

Examples

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

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

Matrix_file <- system.file(file.path("extdata", 
"Sexton2012_yaffetanay_CisTrans_100000_corrected_chr2L.txt.gz"), 
package = "HiCBricks")

Brick_load_matrix(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", matrix_file = Matrix_file, delim = " ", 
remove_prior = TRUE, resolution = 100000)

Brick_matrix_maxdist(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", resolution = 100000)

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