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,
        constrain.region = NULL, batch.size = 500, FUN = NULL)

### Arguments

`Brick` | Required. A string specifying the path to the Brick store created with CreateBrick.
`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.
`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

    Brick.file <- system.file("extdata", "test.hdf", package = "HiCBricks")
    Brick_get_values_by_distance(Brick = Brick.file, chr = "chr19",
    distance = 0)

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

    Brick.file <- system.file("extdata", "test.hdf", package = "HiCBricks")
    Brick_get_values_by_distance(Brick = Brick.file, chr = "chr19",
    distance = 4, FUN = Failsafe_median)

[Package HiCBricks version 1.2.0 Index]