BrickContainer_list_files: Get the list of HDF files present in the Brick container.

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

Description

BrickContainer_list_files fetches the list of HDF files associated to a particular BrickContainer

Usage

BrickContainer_list_files(
    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 5 column tibble containing chromosome pairs, Hi-C resolution, the type of Hi-C matrix and the path to a particular Hi-C matrix file.

Examples

Bintable.path <- system.file("extdata",
"Bintable_100kb.bins", package = "HiCBricks")
out_dir <- file.path(tempdir(), "BrickContainer_list_file_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_list_files(Brick = My_BrickContainer, chr1 = "chr2L",
chr2 = NA)

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