Brick_get_matrix {HiCBricks} | R Documentation

## Return a matrix subset.

### Description

`Brick_get_matrix` will fetch a matrix subset between row values ranging from min(x_coords) to max(x_coords) and column values ranging from min(x_coords) to max(x_coords)

### Usage

    Brick_get_matrix(
        Brick,
        chr1,
        chr2,
        x_coords,
        y_coords,
        resolution,
        force = FALSE,
        FUN = NULL
    )

### 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
`x_coords` | Required. A one-dimensional numeric vector specifying the rows to subset.
`y_coords` | Required. A one-dimensional numeric vector specifying the columns to subset.
`resolution` | Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
`force` | Optional. Default FALSE If true, will force the retrieval operation when matrix contains loaded data until a certain distance.
`FUN` | Optional. If provided a data transformation with FUN will be applied before the matrix is returned.

### Value

Returns a matrix of dimension x_coords length by y_coords length. This may differ based on the operations with FUN.

### See Also

`Brick_get_matrix_within_coords` to get matrix by using matrix genomic coordinates, `Brick_get_values_by_distance` to get values separated at a certain distance, `Brick_fetch_row_vector` to getvalues in a certain row/col and subset them, `Brick_get_vector_values` to get values using matrix coordinates.

### Examples

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

    out_dir <- file.path(tempdir(), "get_matrix_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(Brick = My_BrickContainer, chr1 = "chr2L", chr2 = "chr2L",
    x_coords = c(1:10), y_coords = c(1:10), resolution = 100000)

[Package HiCBricks version 1.5.5 Index]