Brick_load_matrix {HiCBricks}R Documentation

Load a NxM dimensional matrix into the Brick store.

Description

Load a NxM dimensional matrix into the Brick store.

Usage

Brick_load_matrix(Brick, chr1, chr2, matrix.file, delim = " ", exec,
    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 CreateBrick.

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

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.

exec

Required. A string specifying the program to use for reading the file. Use cat for txt files, for bz2 files use bzcat and for gz files zcat.

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 read, in each chunk.

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("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_matrix(Brick = Path_to_cached_file, chr1 = "chr19", 
chr2 = "chr19", matrix.file = Matrix.file, delim = " ", exec = "cat",
remove.prior = TRUE)


[Package HiCBricks version 1.2.0 Index]