Brick_get_entire_matrix: Return an entire matrix for provided chromosome pair for a...

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

Description

Brick_get_entire_matrix will return the entire matrix for the entire chromosome pair provided an object of class BrickContainer, and values for chr1, chr2 and resolution values.

Usage

Brick_get_entire_matrix(Brick, chr1, chr2, resolution)

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 an object of class matrix with dimensions corresponding to chr1 binned length by chr2 binned length.

Examples

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

out_dir <- file.path(tempdir(), "get_vector_val_test")
if(!file.exists(out_dir)){
    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)

Entire_matrix <- Brick_get_entire_matrix(Brick = My_BrickContainer, 
chr1 = "chr2L", chr2 = "chr2L", resolution = 100000)

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