Brick_matrix_issparse: Check if a matrix for a chromosome pair is sparse.

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

Check if a matrix for a chromosome pair is sparse.

Description

Check if a matrix for a chromosome pair is sparse.

Usage

Brick_matrix_issparse(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 a logical vector of length 1, specifying if a matrix was loaded as a sparse matrix.

Examples

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

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

koustav-pal/HiCBlocks documentation built on Oct. 29, 2022, 8:17 a.m.