Brick_get_matrix_mcols: Get the matrix metadata columns in the Brick store.

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

Get the matrix metadata columns in the Brick store.

Description

Brick_get_matrix_mcols will get the specified matrix metadata column for a chr1 vs chr2 Hi-C data matrix. Here, chr1 represents the rows and chr2 represents the columns of the matrix. For cis Hi-C matrices, where chr1 == chr2, chr2_bin_coverage and chr2_col_sums equals chr1_bin_coverage and chr1_row_sums respectively.

Usage

Brick_get_matrix_mcols(
    Brick,
    chr1,
    chr2,
    resolution,
    what = c("chr1_bin_coverage", "chr2_bin_coverage", "chr1_row_sums", "chr2_col_sums")
)

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
what	Required A character vector of length 1 specifying the matrix metric to retrieve

Details

These metadata columns are:

• chr1_bin_coverage: Percentage of rows containing non-zero values

• chr2_bin_coverage: Percentage of columns containing non-zero values

• chr1_row_sums: Total signal (if normalised) or number of reads (if counts) in each row.

• chr2_col_sums: Total signal (if normalised) or number of reads (if counts) in each column.

Value

Returns a 1xN dimensional vector containing the specified matrix metric

Examples

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

out_dir <- file.path(tempdir(), "get_matrix_mcols_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_matrix(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", matrix_file = Matrix_file, delim = " ", 
remove_prior = TRUE, resolution = 100000)

Brick_get_matrix_mcols(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", resolution = 100000, what = "chr1_bin_coverage")

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