Brick_get_values_by_distance: Return values separated by a certain distance.

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

Description

Brick_get_values_by_distance can fetch values with or without transformation or subsetted by a certain distance. Please note, this module is not an iterable module.

Usage

Brick_get_values_by_distance(
    Brick,
    chr,
    distance,
    resolution,
    constrain_region = NULL,
    batch_size = 500,
    FUN = NULL
)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
chr	Required. A string specifying the chromosome for the cis Hi-C matrix from which values will be retrieved at a certain distance.
distance	Required. 0 based. Fetch values separated by distance.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
constrain_region	Optional. A character vector of length 1 with the form chr:start:end specifying the region for which the distance values must be retrieved.
batch_size	Optional. Default 500 A numeric vector of length 1 specifying the size of the chunk to retrieve for diagonal selection.
FUN	Optional. If provided a data transformation with FUN will be applied before values are returned.

Value

Returns a numeric vector of length N depending on the presence of constrain_region, FUN and distance from the main diagonal.

See Also

Brick_get_matrix_within_coords to get matrix by using matrix coordinates, Brick_fetch_row_vector to get values in a certain row/col and subset them, Brick_get_vector_values to get values using matrix coordinates, 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(), "val_by_dist_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_values_by_distance(Brick = My_BrickContainer, chr = "chr2L",
distance = 0, resolution = 100000)

Failsafe_median <- function(x){
     x[is.nan(x) | is.infinite(x) | is.na(x)] <- 0
     return(median(x))
}

Brick_get_values_by_distance(Brick = My_BrickContainer, chr = "chr2L", 
resolution = 100000, distance = 4, FUN = Failsafe_median)

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