R.huge: Methods for Accessing Huge Amounts of Data [deprecated]

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.)

Install the latest version of this package by entering the following in R:
AuthorHenrik Bengtsson [aut, cre, cph]
Date of publication2015-02-22 20:52:32
MaintainerHenrik Bengtsson <henrikb@braju.com>
LicenseLGPL (>= 2.1)

View on CRAN

Man pages

000-LB-.FileMatrix: Gets a subset of elements of a file matrix

000-LB-.FileVector: Gets a subset of elements of a file vector

000-LB-LT_-.FileMatrix: Assigns values to a subset of elements of a file matrix

000-LB-LT_-.FileVector: Assigns values to a subset of elements of a file vector

AbstractFileArray: Class representing a persistent array stored in a file

as.character.AbstractFileArray: Returns a short string describing the file array

as.character.FileMatrix: Returns a short string describing the file matrix

as.matrix.FileMatrix: Returns the elements of a file matrix as an R matrix

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

clone.AbstractFileArray: Clones a file array

close.AbstractFileArray: Closes a connection to the data file of the file array

colnames.FileMatrix: Gets the column names of a file matrix

delete.AbstractFileArray: Deletes the file array from the file system

dim.AbstractFileArray: Gets the dimension of the file array

dimnames.AbstractFileArray: Gets the dimension names of a file array

FileMatrix: Class representing a persistent matrix stored in a file

FileVector: Class representing a persistent vector stored on file

finalize.AbstractFileArray: Internal: Clean up when file array is deallocated from memory

flush.AbstractFileArray: Internal: Flushes the write buffer

getBasename.AbstractFileArray: Gets the basename (filename) of the data file

getByRow.FileMatrix: Checks if elements are stored row by row or not

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

getCloneNumber.AbstractFileArray: Gets the clone number of the file array

getComments.AbstractFileArray: Gets the comments for this file array

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

getDimensionOrder.AbstractFileArray: Gets the order of dimension

getExtension.AbstractFileArray: Gets the filename extension of the file array

getFileSize.AbstractFileArray: Gets the size of the file array

getName.AbstractFileArray: Gets the name of the file array

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

getPathname.AbstractFileArray: Gets the full pathname to the data file

getSizeOfComments.AbstractFileArray: Gets the number of bytes the comments occupies

getSizeOfData.AbstractFileArray: Gets the size of the data section in bytes

getStorageMode.AbstractFileArray: Gets the storage mode of the file array

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

names.FileVector: Gets the element names of a file vector

ncol.FileMatrix: Gets the number of columns of the matrix

Non-documented_objects: Non-documented objects

nrow.FileMatrix: Gets the number of rows of the matrix

open.AbstractFileArray: Opens a connection to the data file of the file array

readAllValues.AbstractFileArray: Reads all values in the file array

readContiguousValues.AbstractFileArray: Reads sets of contiguous values in the file array

readHeader.AbstractFileArray: Read the header of a file array data file

readValues.AbstractFileArray: Reads individual values in the file array

R.huge-package: Package R.huge

rowMeans.FileMatrix: Calculates the means for each row

rownames.FileMatrix: Gets the row names of a file matrix

rowSums.FileMatrix: Calculates the sum for each row

setComments.AbstractFileArray: Sets the comments for this file array

writeAllValues.AbstractFileArray: Writes all values to a file array

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

writeHeader.AbstractFileArray: Writes the header of a file array to file

writeValues.AbstractFileArray: Writes values to a file array


AbstractFileArray Man page
AbstractFileArray.as.character Man page
AbstractFileArray.as.vector Man page
AbstractFileArray.clone Man page
AbstractFileArray.close Man page
AbstractFileArray.delete Man page
AbstractFileArray.dim Man page
AbstractFileArray.dimnames Man page
AbstractFileArray.finalize Man page
AbstractFileArray.flush Man page
AbstractFileArray.getBasename Man page
AbstractFileArray.getBytesPerCell Man page
AbstractFileArray.getCloneNumber Man page
AbstractFileArray.getComments Man page
AbstractFileArray.getDataOffset Man page
AbstractFileArray.getDimensionOrder Man page
AbstractFileArray.getExtension Man page
AbstractFileArray.getFileSize Man page
AbstractFileArray.getName Man page
AbstractFileArray.getPath Man page
AbstractFileArray.getPathname Man page
AbstractFileArray.getSizeOfComments Man page
AbstractFileArray.getSizeOfData Man page
AbstractFileArray.getStorageMode Man page
AbstractFileArray.isOpen Man page
AbstractFileArray.length Man page
AbstractFileArray.open Man page
AbstractFileArray.readAllValues Man page
AbstractFileArray.readContiguousValues Man page
AbstractFileArray.readHeader Man page
AbstractFileArray.readValues Man page
AbstractFileArray.setComments Man page
AbstractFileArray.writeAllValues Man page
AbstractFileArray.writeEmptyData Man page
AbstractFileArray.writeHeader Man page
AbstractFileArray.writeValues Man page
as.character.AbstractFileArray Man page
as.character,AbstractFileArray-method Man page
as.character.FileMatrix Man page
as.character,FileMatrix-method Man page
as.matrix.FileMatrix Man page
as.matrix,FileMatrix-method Man page
as.vector.AbstractFileArray Man page
as.vector,AbstractFileArray-method Man page
clone Man page
clone.AbstractFileArray Man page
clone,AbstractFileArray-method Man page
close Man page
close.AbstractFileArray Man page
close,AbstractFileArray-method Man page
colnames Man page
colnames.default Man page
colnames.FileMatrix Man page
colnames,FileMatrix-method Man page
delete Man page
delete.AbstractFileArray Man page
delete,AbstractFileArray-method Man page
dim.AbstractFileArray Man page
dim,AbstractFileArray-method Man page
dimnames.AbstractFileArray Man page
dimnames,AbstractFileArray-method Man page
FileByteMatrix Man page
FileByteVector Man page
FileDoubleMatrix Man page
FileDoubleVector Man page
FileFloatMatrix Man page
FileFloatVector Man page
FileIntegerMatrix Man page
FileIntegerVector Man page
FileMatrix Man page
[<-.FileMatrix Man page
[.FileMatrix Man page
FileMatrix.[ Man page
FileMatrix.[<- Man page
FileMatrix.as.character Man page
FileMatrix.as.matrix Man page
FileMatrix.colnames Man page
FileMatrix.getByRow Man page
[<-,FileMatrix-method Man page
[,FileMatrix-method Man page
FileMatrix.ncol Man page
FileMatrix.nrow Man page
FileMatrix.rowMeans Man page
FileMatrix.rownames Man page
FileMatrix.rowSums Man page
FileShortMatrix Man page
FileShortVector Man page
FileVector Man page
[<-.FileVector Man page
[.FileVector Man page
FileVector.[ Man page
FileVector.[<- Man page
[<-,FileVector-method Man page
[,FileVector-method Man page
FileVector.names Man page
finalize Man page
finalize.AbstractFileArray Man page
finalize,AbstractFileArray-method Man page
flush Man page
flush.AbstractFileArray Man page
flush,AbstractFileArray-method Man page
getBasename Man page
getBasename.AbstractFileArray Man page
getBasename,AbstractFileArray-method Man page
getByRow Man page
getByRow.FileMatrix Man page
getByRow,FileMatrix-method Man page
getBytesPerCell Man page
getBytesPerCell.AbstractFileArray Man page
getBytesPerCell,AbstractFileArray-method Man page
getCloneNumber Man page
getCloneNumber.AbstractFileArray Man page
getCloneNumber,AbstractFileArray-method Man page
getColumnOffset Man page
getColumnOffset.FileMatrix Man page
getComments Man page
getComments.AbstractFileArray Man page
getComments,AbstractFileArray-method Man page
getDataOffset Man page
getDataOffset.AbstractFileArray Man page
getDataOffset,AbstractFileArray-method Man page
getDimensionOrder Man page
getDimensionOrder.AbstractFileArray Man page
getDimensionOrder,AbstractFileArray-method Man page
getExtension Man page
getExtension.AbstractFileArray Man page
getExtension,AbstractFileArray-method Man page
getFileSize Man page
getFileSize.AbstractFileArray Man page
getFileSize,AbstractFileArray-method Man page
getMatrixIndicies Man page
getMatrixIndicies.FileMatrix Man page
getName Man page
getName.AbstractFileArray Man page
getName,AbstractFileArray-method Man page
getOffset Man page
getOffset.FileMatrix Man page
getPath Man page
getPath.AbstractFileArray Man page
getPath,AbstractFileArray-method Man page
getPathname Man page
getPathname.AbstractFileArray Man page
getPathname,AbstractFileArray-method Man page
getRowOffset Man page
getRowOffset.FileMatrix Man page
getSizeOfComments Man page
getSizeOfComments.AbstractFileArray Man page
getSizeOfComments,AbstractFileArray-method Man page
getSizeOfData Man page
getSizeOfData.AbstractFileArray Man page
getSizeOfData,AbstractFileArray-method Man page
getStorageMode Man page
getStorageMode.AbstractFileArray Man page
getStorageMode,AbstractFileArray-method Man page
isOpen Man page
isOpen.AbstractFileArray Man page
isOpen,AbstractFileArray-method Man page
length.AbstractFileArray Man page
length,AbstractFileArray-method Man page
names.FileVector Man page
names,FileVector-method Man page
ncol Man page
ncol.default Man page
ncol.FileMatrix Man page
ncol,FileMatrix-method Man page
Non-documented objects Man page
nrow Man page
nrow.default Man page
nrow.FileMatrix Man page
nrow,FileMatrix-method Man page
open Man page
open.AbstractFileArray Man page
open,AbstractFileArray-method Man page
readAllValues Man page
readAllValues.AbstractFileArray Man page
readAllValues,AbstractFileArray-method Man page
readContiguousValues Man page
readContiguousValues.AbstractFileArray Man page
readContiguousValues,AbstractFileArray-method Man page
readFullMatrix Man page
readFullMatrix.FileMatrix Man page
readHeader Man page
readHeader.AbstractFileArray Man page
readHeader,AbstractFileArray-method Man page
readValues Man page
readValues.AbstractFileArray Man page
readValues,AbstractFileArray-method Man page
readValues.FileMatrix Man page
R.huge Man page
R.huge-package Man page
rowMeans Man page
rowMeans.default Man page
rowMeans.FileMatrix Man page
rowMeans,FileMatrix-method Man page
rownames Man page
rownames.default Man page
rownames.FileMatrix Man page
rownames,FileMatrix-method Man page
rowSums Man page
rowSums.default Man page
rowSums.FileMatrix Man page
rowSums,FileMatrix-method Man page
setComments Man page
setComments.AbstractFileArray Man page
setComments,AbstractFileArray-method Man page
writeAllValues Man page
writeAllValues.AbstractFileArray Man page
writeAllValues,AbstractFileArray-method Man page
writeEmptyData Man page
writeEmptyData.AbstractFileArray Man page
writeEmptyData,AbstractFileArray-method Man page
writeHeader Man page
writeHeader.AbstractFileArray Man page
writeHeader,AbstractFileArray-method Man page
writeHeaderComments Man page
writeHeaderComments.AbstractFileArray Man page
writeValues Man page
writeValues.AbstractFileArray Man page
writeValues,AbstractFileArray-method Man page
writeValues.FileMatrix Man page


tests/FileByteVector.R tests/FileMatrix,bug20070821.R tests/FileMatrix,bug20070719.R
R/FileByteVector.R R/000.R R/FileShortVector.R R/FileVector.R R/FileDoubleVector.R R/FileByteMatrix.R R/FileIntegerVector.R R/FileFloatMatrix.R R/FileDoubleMatrix.R R/FileIntegerMatrix.R R/AbstractFileArray.R R/FileFloatVector.R R/006.fixVarArgs.R R/FileShortMatrix.R R/seekCon.R R/999.NonDocumentedObjects.R R/999.package.R R/FileMatrix.R R/zzz.R
man/AbstractFileArray.Rd man/names.FileVector.Rd man/getDimensionOrder.AbstractFileArray.Rd man/readAllValues.AbstractFileArray.Rd man/getBytesPerCell.AbstractFileArray.Rd man/setComments.AbstractFileArray.Rd man/writeValues.AbstractFileArray.Rd man/ncol.FileMatrix.Rd man/000-LB-.FileVector.Rd man/getFileSize.AbstractFileArray.Rd man/open.AbstractFileArray.Rd man/rownames.FileMatrix.Rd man/as.character.AbstractFileArray.Rd man/getSizeOfData.AbstractFileArray.Rd man/writeAllValues.AbstractFileArray.Rd man/readHeader.AbstractFileArray.Rd man/as.vector.AbstractFileArray.Rd man/000-LB-LT_-.FileVector.Rd man/000-LB-LT_-.FileMatrix.Rd man/finalize.AbstractFileArray.Rd man/flush.AbstractFileArray.Rd man/getDataOffset.AbstractFileArray.Rd man/FileMatrix.Rd man/getCloneNumber.AbstractFileArray.Rd man/getExtension.AbstractFileArray.Rd man/getName.AbstractFileArray.Rd man/delete.AbstractFileArray.Rd man/getStorageMode.AbstractFileArray.Rd man/getComments.AbstractFileArray.Rd man/rowMeans.FileMatrix.Rd man/dimnames.AbstractFileArray.Rd man/writeHeader.AbstractFileArray.Rd man/isOpen.AbstractFileArray.Rd man/getPath.AbstractFileArray.Rd man/readValues.AbstractFileArray.Rd man/FileVector.Rd man/getPathname.AbstractFileArray.Rd man/000-LB-.FileMatrix.Rd man/as.character.FileMatrix.Rd man/nrow.FileMatrix.Rd man/R.huge-package.Rd man/colnames.FileMatrix.Rd man/getBasename.AbstractFileArray.Rd man/clone.AbstractFileArray.Rd man/close.AbstractFileArray.Rd man/getSizeOfComments.AbstractFileArray.Rd man/rowSums.FileMatrix.Rd man/length.AbstractFileArray.Rd man/writeEmptyData.AbstractFileArray.Rd man/getByRow.FileMatrix.Rd man/as.matrix.FileMatrix.Rd man/readContiguousValues.AbstractFileArray.Rd man/dim.AbstractFileArray.Rd man/Non-documented_objects.Rd

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