Brick_fetch_row_vector: Return row or col vectors.

In koustav-pal/HiCLegos: Framework for Storing and Accessing Hi-C Data Through HDF Files

Return row or col vectors.

Description

Brick_fetch_row_vector will fetch any given rows from a matrix. If required, the rows can be subsetted on the columns and transformations applied. Vice versa is also true, wherein columns can be retrieved and rows subsetted.

Usage

Brick_fetch_row_vector(
    Brick,
    chr1,
    chr2,
    resolution,
    by = c("position", "ranges"),
    vector,
    regions = NULL,
    force = FALSE,
    flip = 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
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
by	Required. One of two possible values, "position" or "ranges". A one-dimensional numeric vector of length 1 specifying one of either position or ranges.
vector	Required. If by is position, a 1 dimensional numeric vector containing the rows to be extracted is expected. If by is ranges, a 1 dimensional character vector containing the names of the bintable is expected. This function does not do overlaps. Rather it returns any given row or column based on their position or names in the bintable.
regions	Optional. Default NULL A character vector of length vector is expected. Each element must be of the form chr:start:end. These regions will be converted back to their original positions and the corresponding rows will be subsetted by the corresponding region element. If the length of regions does not match, the subset operation will not be done and all elements from the rows will be returned.
force	Optional. Default FALSE If true, will force the retrieval operation when matrix contains loaded data until a certain distance.
flip	Optional. Default FALSE If present, will flip everything. This is equivalent to selecting columns, and subsetting on the rows.
FUN	Optional. Default NULL If provided a data transformation with FUN will be applied before the matrix is returned.

Value

Returns a list of length vector. Each list element will be of length chr2 binned length or if regions is present the corresponding region 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 get values in a certain row/col and subset them, Brick_get_matrix to get matrix by using matrix coordinates.

Examples

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

out_dir <- file.path(tempdir(), "get_row_vector_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)

Coordinate <- c("chr2L:1:100000","chr2L:100001:200000")
Test_Run <- Brick_fetch_row_vector(Brick = My_BrickContainer,
chr1 = "chr2L", chr2 = "chr2L", resolution = 100000, 
by = "ranges", vector = Coordinate,
regions = c("chr2L:1:1000000", "chr2L:40001:2000000"))

koustav-pal/HiCLegos documentation built on Nov. 5, 2022, 5:49 p.m.