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.vector) to max(x.vector) and column values ranging from min(x.vector) to max(x.vector)

Usage

Brick_get_matrix(Brick, chr1, chr2, x.vector, y.vector, force = FALSE,
    FUN = NULL)

Arguments

Brick

Required. A string specifying the path to the Brick store created with CreateBrick.

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.vector

Required. A one-dimensional numeric vector specifying the rows to subset.

y.vector

Required. A one-dimensional numeric vector specifying the columns to subset.

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.vector length by y.vector 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

Brick.file <- system.file("extdata", "test.hdf", package = "HiCBricks")
Brick_get_matrix(Brick = Brick.file, chr1 = "chr19", chr2 = "chr19",
x.vector = c(1:10), y.vector = c(1:10))


[Package HiCBricks version 1.2.0 Index]