Brick_load_cis_matrix_till_distance {HiCBricks} | R Documentation |
Load a NxN dimensional sub-distance cis matrix into the Brick store.
Brick_load_cis_matrix_till_distance(Brick, chr, 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 CreateBrick. |
chr |
Required. A character vector of length 1 specifying the chromosome corresponding to the rows and cols of the matrix |
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("extdata", "Bintable_40kb.txt", package = "HiCBricks") Chromosomes <- "chr19" Path_to_cached_file <- CreateBrick(ChromNames = Chromosomes, BinTable = Bintable.path, bin.delim = " ", Output.Filename = file.path(tempdir(),"test.hdf"), exec = "cat", remove.existing = TRUE) Test.mat <- matrix(runif(800*800),nrow = 800, ncol = 800) Matrix.file <- file.path(tempdir(),"Test_matrix.txt") write.table(x = Test.mat, file = Matrix.file, sep = " ", quote = FALSE, row.names = FALSE, col.names = FALSE) Brick_load_cis_matrix_till_distance(Brick = Path_to_cached_file, chr = "chr19", matrix.file = Matrix.file, delim = " ", distance = 200, remove.prior = TRUE)