Description Usage Arguments Value Examples
View source: R/Brick_functions.R
Brick_get_entire_matrix
will return the entire matrix for the entire
chromosome pair provided an object of class BrickContainer, and values for
chr1, chr2 and resolution values.
1 | Brick_get_entire_matrix(Brick, chr1, chr2, resolution)
|
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 |
Returns an object of class matrix with dimensions corresponding to chr1 binned length by chr2 binned length.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"),
package = "HiCBricks")
out_dir <- file.path(tempdir(), "get_vector_val_test")
if(!file.exists(out_dir)){
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)
Entire_matrix <- Brick_get_entire_matrix(Brick = My_BrickContainer,
chr1 = "chr2L", chr2 = "chr2L", resolution = 100000)
|
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