Brick_load_matrix: Load a NxM dimensional matrix into the Brick store.

Description Usage Arguments Value Examples

View source: R/Brick_functions.R

Description

Load a NxM dimensional matrix into the Brick store.

Usage

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Brick_load_matrix(
    Brick = NA,
    chr1 = NA,
    chr2 = NA,
    resolution = NA,
    matrix_file = NA,
    delim = " ",
    remove_prior = FALSE,
    num_rows = 2000,
    is_sparse = FALSE,
    sparsity_bins = 100
)

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

matrix_file

Required. A character vector of length 1 specifying the name of the file to load as a matrix into the Brick store.

delim

Optional. Default " " The delimiter of the matrix file.

remove_prior

Optional. Default FALSE If a matrix was loaded before, it will not be replaced. Use remove_prior to override and replace the existing matrix.

num_rows

Optional. Default 2000 Number of rows to read, in each chunk.

is_sparse

Optional. Default FALSE If true, designates the matrix as being a sparse matrix, and computes the sparsity.index. The sparsity index measures the proportion of non-zero rows or columns at a certain distance from the diagonal (100) in cis interaction matrices.

sparsity_bins

Optional. Default 100 With regards to computing the sparsity.index, this parameter decides the number of bins to scan from the diagonal.

Value

Returns TRUE if all went well.

Examples

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

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

koustav-pal/HiCBlocks documentation built on Jan. 6, 2022, 2:36 a.m.