R: Load a matrix to FlashR.

fm.get.matrix

R Documentation

Load a matrix to FlashR.

Description

There are many different ways of loading a matrix to FlashR. fm.load.dense.matrix loads a dense matrix in the text format from the Linux filesystem. fm.load.dense.matrix.bin loads a dense matrix in the binary format from the Linux filesystem. fm.load.sparse.matrix loads a FlashR sparse matrix from files. The matrix in the file is in the FlashR format. fm.get.dense.matrix returns a named dense matrix that has already been loaded to FlashR.

Usage

fm.get.dense.matrix(name)

fm.load.dense.matrix(src.file, in.mem, ele.type = "D", delim = ",",
  ncol = .Machine$integer.max, name = "")

fm.load.dense.matrix.bin(src.file, in.mem, nrow, ncol, byrow, ele.type,
  name = "")

fm.load.sparse.matrix(file, in.mem = TRUE, is.sym = FALSE, ele.type = "B",
  delim = ",", name = "")

fm.load.sparse.matrix.bin(spm, spm.idx, t.spm = NULL, t.spm.idx = NULL,
  in.mem = TRUE)

Arguments

`name`	a string indicating the name of the dense matrix after being loaded to FlashR.
`src.file`	a string that indicates the file in the Linux filesystem that stores data to be loaded to FlashR.
`in.mem`	Determine the loaded matrix is stored in memory or on SAFS.
`ele.type`	A string that represents the element type in a matrix. "B" means binary, "I" means integer, "L" means long integer, "F" means single-precision floating point, "D" means double-precision floating point.
`delim`	The delimiter of separating elements in the text format.
`ncol`	the number of columns in the binary dense matrix.
`nrow`	the number of rows in the binary dense matrix.
`byrow`	a logical value indicating if the data in the binary matrix is stored by rows.
`spm`	The file that stores the sparse matrix.
`spm.idx`	The file that stores the index of the sparse matrix.
`t.spm`	The file that stores the transpose of the sparse matrix.
`t.spm.idx`	The file that stores the index of the transpose of the sparse matrix.

Details

If a user provides name and in.mem is TRUE, the created vector/matrix will be kept on disks persistently. That is, even if a user exits from R, the vector/matrix will still be kept on disks. A user can access to the dense matrix with fm.get.dense.matrix the next time when he/she opens FlashR.

Value

a FlashR matrix.

Author(s)

Da Zheng <dzheng5@jhu.edu>

Examples

mat <- fm.get.dense.matrix("mat123")	# get a dense matrix named "mat123", stored in SAFS.
mat <- fm.load.dense.matrix("./mat123.cvs", TRUE) # load a dense matrix from a local file "mat123.cvs" to memory.
mat <- fm.load.sparse.matrix("./spm123.mat", "./spm123.mat_idx") # load a symmetric sparse matrix in FlashMatrix format (whose data is stored in "spm123.mat" and the index is stored in "spm123.mat_idx") to memory.