Brick_get_values_by_distance {HiCBricks} | R Documentation

## Return values separated by a certain distance.

### 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)

[Package HiCBricks version 1.4.0 Index]