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R.huge (version 0.9.0)

Methods for Accessing Huge Amounts of Data [deprecated]

Description

DEPRECATED. Do not start building new projects based on this package. Cross-platform alternatives are the following packages: bigmemory (CRAN), ff (CRAN), BufferedMatrix (Bioconductor). The main usage of it was inside the aroma.affymetrix package. (The package currently provides a class representing a matrix where the actual data is stored in a binary format on the local file system. This way the size limit of the data is set by the file system and not the memory.)

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Install

install.packages('R.huge')

Monthly Downloads

396

Version

0.9.0

License

LGPL (>= 2.1)

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Maintainer

Henrik Bengtsson

Last Published

February 22nd, 2015

Functions in R.huge (0.9.0)

clone.AbstractFileArray

Clones a file array
as.matrix.FileMatrix

Returns the elements of a file matrix as an R matrix
AbstractFileArray

Class representing a persistent array stored in a file
[< -.FileMatrix

Assigns values to a subset of elements of a file matrix
[< -.FileVector

Assigns values to a subset of elements of a file vector
[.FileVector

Gets a subset of elements of a file vector
as.vector.AbstractFileArray

Returns the elements of a file array as an R vector
as.character.AbstractFileArray

Returns a short string describing the file array
[.FileMatrix

Gets a subset of elements of a file matrix
as.character.FileMatrix

Returns a short string describing the file matrix
close.AbstractFileArray

Closes a connection to the data file of the file array
dim.AbstractFileArray

Gets the dimension of the file array
getFileSize.AbstractFileArray

Gets the size of the file array
getByRow.FileMatrix

Checks if elements are stored row by row or not
getCloneNumber.AbstractFileArray

Gets the clone number of the file array
getExtension.AbstractFileArray

Gets the filename extension of the file array
FileVector

Class representing a persistent vector stored on file
getStorageMode.AbstractFileArray

Gets the storage mode of the file array
getBytesPerCell.AbstractFileArray

Gets the number of bytes per element in a file array
getPath.AbstractFileArray

Gets the path (directory) where the data file lives
getDimensionOrder.AbstractFileArray

Gets the order of dimension
rowSums.FileMatrix

Calculates the sum for each row
readContiguousValues.AbstractFileArray

Reads sets of contiguous values in the file array
getComments.AbstractFileArray

Gets the comments for this file array
writeEmptyData.AbstractFileArray

Writes an empty data section to the data file of a file array
flush.AbstractFileArray

Internal: Flushes the write buffer
getName.AbstractFileArray

Gets the name of the file array
getDataOffset.AbstractFileArray

Gets file position of the data section in a file array
dimnames.AbstractFileArray

Gets the dimension names of a file array
finalize.AbstractFileArray

Internal: Clean up when file array is deallocated from memory
colnames.FileMatrix

Gets the column names of a file matrix
isOpen.AbstractFileArray

Checks whether the data file of the file array is open or not
length.AbstractFileArray

Gets the number of elements in a file array
FileMatrix

Class representing a persistent matrix stored in a file
delete.AbstractFileArray

Deletes the file array from the file system
getPathname.AbstractFileArray

Gets the full pathname to the data file
nrow.FileMatrix

Gets the number of rows of the matrix
getBasename.AbstractFileArray

Gets the basename (filename) of the data file
open.AbstractFileArray

Opens a connection to the data file of the file array
rowMeans.FileMatrix

Calculates the means for each row
rownames.FileMatrix

Gets the row names of a file matrix
setComments.AbstractFileArray

Sets the comments for this file array
writeHeader.AbstractFileArray

Writes the header of a file array to file
readAllValues.AbstractFileArray

Reads all values in the file array
Non-documented objects

Non-documented objects
writeValues.AbstractFileArray

Writes values to a file array
getSizeOfData.AbstractFileArray

Gets the size of the data section in bytes
ncol.FileMatrix

Gets the number of columns of the matrix
getSizeOfComments.AbstractFileArray

Gets the number of bytes the comments occupies
readHeader.AbstractFileArray

Read the header of a file array data file
names.FileVector

Gets the element names of a file vector
R.huge-package

Package R.huge
writeAllValues.AbstractFileArray

Writes all values to a file array
readValues.AbstractFileArray

Reads individual values in the file array
[< -.FileMatrix

Assigns values to a subset of elements of a file matrix
[< -.FileVector

Assigns values to a subset of elements of a file vector