Brick_get_vector_values: Return a N dimensional vector selection.

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

Description

Brick_get_vector_values is the base function being used by all other matrix retrieval functions.

Usage

Brick_get_vector_values(
    Brick,
    chr1,
    chr2,
    resolution,
    xaxis,
    yaxis,
    FUN = NULL,
    force = FALSE
)

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
xaxis	Required. A 1 dimensional vector containing the rows to retrieve. Gaps in this vector may result in unexpected behaviour as the values which are considered are min(xaxis) and max(xaxis) for retrieval.
yaxis	Required. A 1 dimensional vector containing the columns to retrieve. Gaps in this vector may result in unexpected behaviour as the values which are considered are min(yaxis) and max(yaxis) for retrieval.
FUN	Optional. Default NULL If provided a data transformation with FUN will be applied before the vector is returned.
force	Optional. Default FALSE If true, will force the retrieval operation when matrix contains loaded data until a certain distance.

Value

Returns a vector of length yaxis if length of xaxis is 1. Else returns a matrix of dimension xaxis length by yaxis length.

Note

Whatever the length of xaxis or yaxis may be, the coordinates under consideration will range from min(xaxis) to max(xaxis) on the rows or min(yaxis) to max(yaxis) on the columns.

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)

Brick_get_vector_values(Brick = My_BrickContainer, chr1 = "chr2L",
chr2 = "chr2L", resolution = 100000, xaxis = c(1:10), yaxis = c(1:10))

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