BufferedMatrix-class {BufferedMatrix}R Documentation

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.

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

Author(s)

B. M. Bolstad bmb@bmbolstad.com


[Package BufferedMatrix version 1.14.0 Index]