Brick_load_matrix {HiCBricks} | R Documentation

## Load a NxM dimensional matrix into the Brick store.

### Description

Load a NxM dimensional matrix into the Brick store.

### Usage

    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

    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)

[Package HiCBricks version 1.8.0 Index]