Brick_matrix_dimensions: Return the dimensions of a matrix

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

Description

Return the dimensions of a matrix

Usage

Brick_matrix_dimensions(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

Value

Returns the dimensions of a Hi-C matrix for any given chromosome pair.

Examples

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

out_dir <- file.path(tempdir(), "matrix_dimension_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_dimensions(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", resolution = 100000)

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