Brick_get_values_by_distance {HiCBricks} | R Documentation |
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.
Brick_get_values_by_distance(Brick, chr, distance, constrain.region = NULL, batch.size = 500, FUN = NULL)
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. |
Returns a numeric vector of length N depending on the presence of constrain.region, FUN and distance from the main diagonal.
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.
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)