Brick_list_matrices {HiCBricks} | R Documentation

## List the matrix pairs present in the Brick store.

### 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)

[Package HiCBricks version 1.4.0 Index]