BufferedMatrix-class: Class BufferedMatrix
In BufferedMatrix: A matrix data storage object held in temporary files

Description Objects from the Class Slots Methods Author(s)

This is a class representation of a buffered matrix (of numeric data). In this case data is primarily stored outide main memory in temporary files.

Objects can be created using the function createBufferedMatrix

rawBufferedMatrix:: a pointer to an external structure used to access and store the matrix data.
rownames:: rownames for the matrix.
colnames:: colnames for the matrix.

ncol: signature(object = "BufferedMatrix"): Returns the number of columns in the matrix
nrow: signature(object = "BufferedMatrix"): Returns the number of rows in the matrix
dim: signature(object = "BufferedMatrix"): Returns the dimensions of the matrix
buffer.dim: signature(object = "BufferedMatrix"): Returns the number of columns and the number of rows to be stored in the buffer
set.buffer.dim: signature(object = "BufferedMatrix"): Set the buffer size or resize it
[: signature(object = "BufferedMatrix"): matrix accessor
[<-: signature(object = "BufferedMatrix"): matrix replacer
show: signature(object = "BufferedMatrix"): prints basic information about the BufferedMatrix out to screen
is.RowMode: signature(object = "BufferedMatrix"): returns TRUE if the row buffer is active and FALSE otherwise.
is.ColMode: signature(object = "BufferedMatrix"): returns TRUE if the row buffer is inactive and FALSE otherwise.
RowMode: signature(object = "BufferedMatrix"): Activate the row buffer.
ColMode: signature(object = "BufferedMatrix"): Deactivate the row buffer
duplicate: signature(object = "BufferedMatrix"): Make a copy of the BufferedMatrix
prefix: signature(object = "BufferedMatrix"): return the initial part of the string used for temporary files
directory: signature(object = "BufferedMatrix"): return the location where temporary files are stored
filenames: signature(object = "BufferedMatrix"): return the fully pathed filenames for each column in the matrix
ewApply: signature(object = "BufferedMatrix"): apply a function elementwise
exp: signature(object = "BufferedMatrix"): Compute the exponential elementwise of the matrix
sqrt: signature(object = "BufferedMatrix"): Compute the square-root elementwise of the matrix
pow: signature(object = "BufferedMatrix"): Compute $x^power$ elementwise of the matrix
log: signature(object = "BufferedMatrix"): Compute logarithm elementwise of the matrix
colMax: signature(object = "BufferedMatrix"): Returns a vector containing maximums by column
rowMax: signature(object = "BufferedMatrix"): Returns a vector containing maximums by row
colMeans: signature(object = "BufferedMatrix"): Returns a vector containing means by column
rowMeans: signature(object = "BufferedMatrix"): Returns a vector containing means by row
colMin: signature(object = "BufferedMatrix"): Returns a vector containing minimums by column
rowMin: signature(object = "BufferedMatrix"): Returns a vector containing minimums by row
colVars: signature(object = "BufferedMatrix"): Returns a vector containing sample variances by column
rowVars: signature(object = "BufferedMatrix"): Returns a vector containing sample variances by row
colSd: signature(object = "BufferedMatrix"): Returns a vector containing sample standard deviations by column
rowSd: signature(object = "BufferedMatrix"): Returns a vector containing sample standard deviations by row
colSums: signature(object = "BufferedMatrix"): Returns a vector containing sum by column
rowSums: signature(object = "BufferedMatrix"): Returns a vector containing sum by row
colMedians: signature(object = "BufferedMatrix"): Returns a vector containing medians by column
rowMedians: signature(object = "BufferedMatrix"): Returns a vector containing medians by row. Best only used when the matrix is in RowMode (otherwise it is extremely slow)
Max: signature(object = "BufferedMatrix"): Returns the maximum of all elements in the matrix
Min: signature(object = "BufferedMatrix"): Returns the minimum of all elements in the matrix
Var: signature(object = "BufferedMatrix"): Returns the sample variance of all elements in the matrix
Sd: signature(object = "BufferedMatrix"): Returns the sample standard deviations of all elements in the matrix
Sum: signature(object = "BufferedMatrix"): Returns the sum of all elements in the matrix
mean: signature(object = "BufferedMatrix"): Returns the mean of all elements in the matrix
colApply: signature(object = "BufferedMatrix"): apply a function columnwise. Returns either a vector or BufferedMatrix.
rowApply: signature(object = "BufferedMatrix"): apply a function row-wise. Returns either a vector or BufferedMatrix.
as.matrix: signature(object = "BufferedMatrix"): coerce BufferedMatrix into a regular R matrix
subBufferedMatrix: signature(object = "BufferedMatrix"): gets data from BufferedMatrix and returns it in another BufferedMatrix
rownames: signature(object = "BufferedMatrix") : access the row names
colnames: signature(object = "BufferedMatrix") : access the column names
rownames<-: signature(object = "BufferedMatrix") : replace the row names
colnames<-: signature(object = "BufferedMatrix") : replace the column names
dimnames: signature(object = "BufferedMatrix") : Access the row and column names
dimnames: signature(object = "BufferedMatrix") : Replace the row and column names
ReadOnlyMode: signature(object = "BufferedMatrix") : Toggles the Read Only mode on and off
is.ReadOnlyMode: signature(object = "BufferedMatrix") : Finds out if it is in Read Only Mode
memory.usage: signature(object = "BufferedMatrix") : Give amount of RAM currently in use by BufferedMatrix object
disk.usage: signature(object = "BufferedMatrix") : Give amount of disk space currently in use by BufferedMatrix object
as(matrix,BufferedMatrix):: Coerce matrix to BufferedMatrix.
as(BufferedMatrix,matrix):: Coerce the Buffered to matrix.
AddColumn:: Add an additional column to the matrix. Will be all empty (set to 0)
MoveStorageDirectory:: Move the temporary files used to store the matrix from one location to another