Brick_load_cis_matrix_till_distance: Load a NxN dimensional sub-distance _cis_ matrix into the...

In koustav-pal/HiCLegos: Framework for Storing and Accessing Hi-C Data Through HDF Files

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

Description

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

Usage

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
)

Arguments

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.

Value

Returns TRUE if all went well.

Examples

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)

koustav-pal/HiCLegos documentation built on Nov. 5, 2022, 5:49 p.m.