Brick_load_data_from_sparse {HiCBricks} | R Documentation

## Identify compartments in the Hi-C data

### Description

`Brick_load_data_from_sparse` loads data from a table like file, such as sparse matrices.

### Usage

    Brick_load_data_from_sparse(
        Brick,
        table_file,
        delim = " ",
        resolution = NULL,
        batch_size = 1e+06,
        matrix_chunk = 2000,
        col_index = c(1, 2, 3),
        remove_prior = FALSE
    )

### Arguments

`Brick` | Required. A string specifying the path to the Brick store created with Create_many_Brick.
`table_file` | Path to the file that will be loaded
`delim` | Optional. Default " " The delimiter of the matrix file.
`resolution` | Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
`batch_size` | Optional Default 1000000 Number of rows to read with each iteration from a sparse matrix.
`matrix_chunk` | Optional Default 2000 The nxn matrix square to fill per iteration to a Brick object.
`col_index` | Optional. Default "c(1,2,3)". A character vector of length 3 containing the indexes of the required columns in the table file. the first index, corresponds to bin1, the second to bin2 and the third to the signal value.
`remove_prior` | Optional. Default FALSE If a matrix was loaded before, it will not be replaced. Use remove_prior to override and replace the existing matrix.

### Value

A dataframe containing the chromosome genomic coordinates and the first three principal components.

### Examples

    ## Not run:
    Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"),
    package = "HiCBricks")

    out_dir <- file.path(tempdir(), "get_vector_val_test")
    if(!file.exists(out_dir)){
        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"),
    remove_file = TRUE, sep = " ",
    resolution = 100000)

    Brick_load_data_from_sparse(Brick = My_BrickContainer,
    table_file = file.path(out_dir, "example_out.txt"),
    delim = " ", resolution = 100000, col_index = c(3,4,5))

    ## End(Not run)

[Package HiCBricks version 1.5.5 Index]