A 'disk.matrix' contains a file path to a matrix stored on disk,
along with meta data for how to read that file. This allows NetRep
to load datasets into RAM only when required, i.e. one at a time. This
significantly reduces the memory usage of R when analysing large datasets.
'disk.matrix' objects may be supplied instead of 'matrix'
objects in the input list arguments 'network', 'data', and
'correlation', which are common to most of NetRep's functions.
attach.disk.matrix(file, serialized = TRUE, ...)serialize.table(file, ...)
is.disk.matrix(x)
as.disk.matrix(x, file, serialize = TRUE)
# S4 method for disk.matrix
as.disk.matrix(x, file, serialize = TRUE)
# S4 method for matrix
as.disk.matrix(x, file, serialize = TRUE)
# S4 method for ANY
as.disk.matrix(x, file, serialize = TRUE)
# S4 method for disk.matrix
as.matrix(x)
# S4 method for disk.matrix
show(object)
A disk.matrix object (attach.disk.matrix, as.disk.matrix),
a matrix (as.matrix), the file path to a serialized matrix
(serialize.table), or a TRUE or FALSE indicating
whether an object is a disk.matrix (is.disk.matrix).
for attach.disk.matrix the file name of a matrix on disk.
For as.disk.matrix the file name to save the matrix to. For
serialize.table the file name of a matrix in table format on disk.
determines how the matrix will be loaded from disk into R
by as.matrix. If TRUE, the readRDS function
will be used. If FALSE, the read.table function will
be used.
arguments to be used by read.table when reading in matrix
data from a file in table format.
for as.matrix a disk.matrix object to load into R.
For as.disk.matrix an object to convert to a disk.matrix. For
is.disk.matrix an object to check if its a disk.matrix.
determines how the matrix is saved to disk by
as.disk.matrix. If TRUE it will be stored as a serialized R
object using saveRDS. If FALSE it will be stored as a
tab-separated file using write.table.
a 'disk.matrix' object.
filethe name of the file where the matrix is saved.
read.funceither "read.table" or "readRDS".
func.argsa list of arguments to be supplied to the 'read.func'.
attach.disk.matrix does not check whether the specified file can be
read into R. as.matrix will fail and throw an error if this is the
case.
Matrices may either be stored as regular table files that can be read by
read.table, or as serialized R objects that can be read by
readRDS. Serialized objects are much faster to load, but
cannot be read by other programs.
The attach.disk.matrix function creates a disk.matrix object
from a file path. The as.matrix function will load the data from disk
into the R session as a regular matrix object.
The as.disk.matrix function converts a matrix into a
disk.matrix by saving its contents to the specified file. The
serialize argument determines whether the data is stored as a
serialized R object or as a tab-separated file (i.e. sep="\t"). We
recommend storing the matrix as a serialized R object unless disk space is
a concern. More control over the storage format can be obtained by using
saveRDS or write.table directly.
The serialize.matrix function converts a file in table format to a
serialized R object with the same file name, but with the ".rds" extension.