Brick_load_cis_matrix_till_distance: Load a NxN dimensional sub-distance _cis_ matrix into the...
In HiCBricks: Framework for Storing and Accessing Hi-C Data Through HDF Files

Description Usage Arguments Value Examples

Load a NxN dimensional sub-distance cis matrix into the Brick store.

Brick_load_cis_matrix_till_distance(
    Brick = NA,
    chr = NA,
    resolution = NA,
    matrix_file,
    delim = " ",
    distance,
    remove_prior = FALSE,
    num_rows = 2000,
    is_sparse = FALSE,
    sparsity_bins = 100
)

`Brick`	Required. A string specifying the path to the Brick store created with Create_many_Brick.
`chr`	Required. A character vector of length 1 specifying the chromosome corresponding to the rows and cols 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
`matrix_file`	Required. A character vector of length 1 specifying the name of the file to load as a matrix into the Brick store.
`delim`	Optional. Default " " The delimiter of the matrix file.
`distance`	Required. Default NULL. For very high-resolution matrices, read times can become extremely slow and it does not make sense to load the entire matrix into the data structure, as after a certain distance, the matrix will become extremely sparse. This ensures that only interactions upto a certain distance from the main diagonal will be loaded into the data structure.
`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.
`num_rows`	Optional. Default 2000 Number of rows to insert per write operation in the HDF file.
`is_sparse`	Optional. Default FALSE If true, designates the matrix as being a sparse matrix, and computes the sparsity.index. The sparsity index measures the proportion of non-zero rows or columns at a certain distance from the diagonal (100) in cis interaction matrices.
`sparsity_bins`	Optional. Default 100 With regards to computing the sparsity.index, this parameter decides the number of bins to scan from the diagonal.

Returns TRUE if all went well.

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

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

Matrix_file <- system.file(file.path("extdata", 
"Sexton2012_yaffetanay_CisTrans_100000_corrected_chr2L.txt.gz"), 
package = "HiCBricks")

Brick_load_cis_matrix_till_distance(Brick = My_BrickContainer, 
chr = "chr2L", resolution = 100000, matrix_file = Matrix_file, 
delim = " ", distance = 30, remove_prior = TRUE)