BufferedMatrix-class: Class BufferedMatrix

Description

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.

Arguments

Objects from the Class

Objects can be created using the function createBufferedMatrix

Slots

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.

Methods

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