Brick_matrix_exists: Check if a chromosome pair exists.

View source: R/Brick_functions.R

Brick_matrix_existsR Documentation

Check if a chromosome pair exists.

Description

Matrices are created when the bintable is loaded and the chromosome names are provided. If a user is in doubt regarding whether a matrix is present or not it is useful to check this function. If the Bintable did not contain a particular chromosome, any matrices for that chromosome would not be present in the file

Usage

Brick_matrix_exists(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 the matrix exists or not.

Examples


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

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


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