BrickContainer_list_files {HiCBricks}R Documentation

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

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)


[Package HiCBricks version 1.4.0 Index]