Brick_get_matrix: Return a matrix subset.

In HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

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)

HiCBricks documentation built on Nov. 8, 2020, 7:45 p.m.