filematrix-class {filematrix}

Manipulating file matrices (class "filematrix")

Description

filematrix is a class for working with very large matrices stored in files, not held in computer memory. It is intended as a simple, efficient solution to handling big numeric data (i.e., datasets larger than memory capacity) in R.
A new filematrix can be created with fm.create. It can be created from an existing R matrix with fm.create.from.matrix. A text file with a matrix can be scanned and converted into a filematrix with fm.create.from.text.file. An existing filematrix can be opened for read/write access with fm.open or loaded fully in memory with fm.load.

A filematrix can be handled as an ordinary matrix in R.

It can be read from and written to via usual indexing with possible omission of indices.
For example: fm[1:3,2:4] and fm[,2:4].

The values can also be accessed as a vector with single indexing.
For example: fm[3:7] and fm[4:7] = 1:4.

A whole filematrix can be read memory as an ordinary R matrix with as.matrix function or empty indexing fm[].

The dimensions of filematrix can be obtained via dim, nrow and ncol functions and modified with dim function.
For example: dim(fm) and dim(fm) = c(10,100).

The number of elements in filematrix is returned by length function.

A filematrix can have row and column names. They can be accessed using the standard functions rownames, colnames, and dimnames.

A filematrix can be closed after use with close command. Note, however, that there is no risk of losing modifications to a filematrix if an object is not closed, as all changes are written to disk without delay.

Usage

## S3 method for class 'filematrix'
x[i,j]
## S3 replacement method for class 'filematrix'
x[i,j] <- value

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

## S4 method for signature 'filematrix'
dim(x)
## S4 replacement method for signature 'filematrix'
dim(x) <- value

## S4 method for signature 'filematrix'
length(x)

## S4 method for signature 'filematrix'
rownames(x)
## S4 replacement method for signature 'filematrix'
rownames(x) <- value

## S4 method for signature 'filematrix'
colnames(x)
## S4 replacement method for signature 'filematrix'
colnames(x) <- value

## S4 method for signature 'filematrix'
dimnames(x)
## S4 replacement method for signature 'filematrix'
dimnames(x) <- value

Arguments

x

A filematrix object (filematrix).

i, j

Row/column indices specifying elements to extract or replace.

value

A new value to replace the indexed element(s).

Value

length function returns the number of elements in the filematrix.

Functions colnames, rownames, and dimnames return the same values as their counterparts for the regular R matrices.

Methods

isOpen

Returns TRUE is the filematrix is open.

readAll():

Return the whole matrix.
Same as fm[] or as.matrix(fm)

writeAll(value):

Fill in the whole matrix.
Same as fm[] = value

readSubCol(i, j, num):

Read num values in column j starting with row i.
Same as fm[i:(i+num-1), j]

writeSubCol(i, j, value):

Write values in the column j starting with row i.
Same as fm[i:(i+length(value)-1), j] = value

readCols(start, num):

Read num columns starting with column start.
Same as fm[, start:(start+num-1)]

writeCols(start, value):

Write columns starting with column start.
Same as fm[, start:(start+ncol(value)-1)] = value

readSeq(start, len):

Read len values from the matrix starting with start-th value.
Same as fm[start:(start+len-1)]

writeSeq(start, value):

Write values in the matrix starting with start-th value.
Same as fm[start:(start+length(value)-1)] = value

appendColumns(mat)

Increases filematrix by adding columns to the right side of the matrix. Matrix mat must have the same number of rows.
Same as fm = cbind(fm, mat) for ordinary matrices.

Author(s)

Andrey A Shabalin [e-mail]

See Also

For function creating and opening file matrices see fm.create.

Run browseVignettes("filematrix") for the list of vignettes.