Brick_load_data_from_sparse: Identify compartments in the Hi-C data

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

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)

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