BrickContainer_get_path_to_file: Get the path to HDF files present in the Brick container.

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

Get the path to HDF files present in the Brick container.

Description

BrickContainer_get_path_to_file fetches the list of HDF file paths associated to a particular BrickContainer

Usage

BrickContainer_get_path_to_file(
    Brick = NULL,
    chr1 = NA,
    chr2 = NA,
    type = NA,
    resolution = NA
)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Bricks.
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
type	A value from one of cis, trans specifying the type of files to list cis will list intra-choromosomal file paths and trans will list inter-chromosomal file paths.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed

Value

A vector containing filepaths

Examples

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

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

BrickContainer_get_path_to_file(Brick = My_BrickContainer, chr1 = "chr2L",
chr2 = "chr2L", resolution = 100000)

koustav-pal/HiCBricks documentation built on Oct. 25, 2022, 12:06 a.m.