Brick_export_to_sparse: Export an entire resolution from a given BrickContainer as a...

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

Export an entire resolution from a given BrickContainer as a upper triangle sparse matrix

Description

Brick_export_to_sparse will accept as input an object of class BrickContainer, a string of length 1 as resolution and a path specifying the output file to write. It writes the content of the all loaded Brick objects as a upper triangle sparse matrix (col > row) containing non-zero values.

Usage

Brick_export_to_sparse(
    Brick,
    out_file,
    remove_file = FALSE,
    resolution,
    sep = " "
)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
out_file	Path to the output file to write.
remove_file	Default FALSE. If a file by the same name is present that file will be removed.
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
sep	column delimiter in output file. Default single space.

Value

Returns a data.frame corresponding to the head of the output file

Examples

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

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

Matrix_file <- system.file(file.path("extdata", 
"Sexton2012_yaffetanay_CisTrans_100000_corrected_chr2L.txt.gz"), 
package = "HiCBricks")

Brick_load_matrix(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", matrix_file = Matrix_file, delim = " ", 
remove_prior = TRUE, resolution = 100000)

Brick_export_to_sparse(Brick = My_BrickContainer, 
out_file = file.path(out_dir, "example_out.txt"), 
resolution = 100000)

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