Brick_get_vector_values {HiCBricks} | R Documentation

## Return a N dimensional vector selection.

### 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))

[Package HiCBricks version 1.10.0 Index]