Brick_get_matrix_mcols {HiCBricks} | R Documentation

## Get the matrix metadata columns in the Brick store.

### Description

`Brick_get_matrix_mcols` will get the specified matrix metadata column for a chr1 vs chr2 Hi-C data matrix. Here, chr1 represents the rows and chr2 represents the columns of the matrix. For cis Hi-C matrices, where chr1 == chr2, chr2_bin_coverage and chr2_col_sums equals chr1_bin_coverage and chr1_row_sums respectively.

### Usage

    Brick_get_matrix_mcols(
        Brick,
        chr1,
        chr2,
        resolution,
        what = c("chr1_bin_coverage", "chr2_bin_coverage", "chr1_row_sums", "chr2_col_sums")
    )

### 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
`what` | Required A character vector of length 1 specifying the matrix metric to retrieve

### Details

These metadata columns are:

- chr1_bin_coverage: Percentage of rows containing non-zero values

- chr2_bin_coverage: Percentage of columns containing non-zero values

- chr1_row_sums: Total signal (if normalised) or number of reads (if counts) in each row.

- chr2_col_sums: Total signal (if normalised) or number of reads (if counts) in each column.

### Value

Returns a 1xN dimensional vector containing the specified matrix metric

### Examples

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

    out_dir <- file.path(tempdir(), "get_matrix_mcols_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_get_matrix_mcols(Brick = My_BrickContainer, chr1 = "chr2L",
    chr2 = "chr2L", resolution = 100000, what = "chr1_bin_coverage")

[Package HiCBricks version 1.5.5 Index]