Brick_list_matrices: List the matrix pairs present in the Brick store.

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

Description

Brick_list_matrices will list all chromosomal pair matrices from the Brick store, with their associated filename, value range, done status and sparse

Usage

Brick_list_matrices(
    Brick,
    chr1 = NA,
    chr2 = NA,
    resolution = NA,
    all_resolutions = FALSE
)

Arguments

Brick	Required. A string specifying the path to the Brick store created with Create_many_Brick.
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
resolution	Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed
all_resolutions	Optional. Default FALSE If resolution is not defined and all_resolutions is TRUE, the resolution parameter will be ignored and the function is executed on all files listed in the Brick container

Value

Returns a data.frame object with columns chr1, chr2 corresponding to chromosome pairs, and the associated attributes. filename corresponds to the name of the file that was loaded for the pair. min and max specify the minimum and maximum values in the matrix, done is a logical value specifying if a matrix has been loaded and sparsity specifies if a matrix is defined as a sparse matrix.

Examples

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

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

Brick_list_matrices(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", resolution = 100000)

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