Brick_export_to_sparse {HiCBricks} | R Documentation

## 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)

[Package HiCBricks version 1.4.0 Index]