Brick_get_entire_matrix {HiCBricks} | R Documentation

## Return an entire matrix for provided chromosome pair for a resolution.

### Description

`Brick_get_entire_matrix` will return the entire matrix for the entire chromosome pair provided an object of class BrickContainer, and values for chr1, chr2 and resolution values.

### Usage

    Brick_get_entire_matrix(Brick, chr1, chr2, resolution)

### 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 an object of class matrix with dimensions corresponding to chr1 binned length by chr2 binned length.

### Examples

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

    out_dir <- file.path(tempdir(), "get_vector_val_test")
    if(!file.exists(out_dir)){
        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)

    Entire_matrix <- Brick_get_entire_matrix(Brick = My_BrickContainer,
    chr1 = "chr2L", chr2 = "chr2L", resolution = 100000)

[Package HiCBricks version 1.6.0 Index]