disk.matrix: The 'disk.matrix' class

In InouyeLab/NetRep: Permutation Testing Network Module Preservation Across Datasets

Description

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.

Usage

attach.disk.matrix(file, serialized = TRUE, ...)

serialize.table(file, ...)

is.disk.matrix(x)

as.disk.matrix(x, file, serialize = TRUE)

## S4 method for signature 'disk.matrix'
as.disk.matrix(x, file, serialize = TRUE)

## S4 method for signature 'matrix'
as.disk.matrix(x, file, serialize = TRUE)

## S4 method for signature 'ANY'
as.disk.matrix(x, file, serialize = TRUE)

## S4 method for signature 'disk.matrix'
as.matrix(x)

## S4 method for signature 'disk.matrix'
show(object)

Arguments

file	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.
serialized	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.
x	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.
serialize	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.
object	a 'disk.matrix' object.

Details

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.

Value

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).

Slots

file

the name of the file where the matrix is saved.

read.func

either "read.table" or "readRDS".

func.args

a list of arguments to be supplied to the 'read.func'.

Warning

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.

InouyeLab/NetRep documentation built on Oct. 8, 2020, 2:32 a.m.