Package 'BufferedMatrix'

Check or Coerce object to BufferedMatrix

Description

'as.BufferedMatrix' will coerce the supplied object into a BufferedMatrix. 'is.BufferedMatrix' checks whether the supplied argument is a BufferedMatrix.

Usage

as.BufferedMatrix(x, bufferrows=1, buffercols=1,directory=getwd())
 is.BufferedMatrix(x)

Arguments

x	an R object
bufferrows	number of rows to be buffered if the row buffer is activated
buffercols	number of columns to be buffered
directory	path to directory where temporary files should be stored

Details

These functions are useful for converting between R matrix objects and BufferedMatrix objects.

Author(s)

B. M. Bolstad <[email protected]>

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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 [email protected]

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createBufferedMatrix

Description

Creates a Buffered Matrix object

Usage

createBufferedMatrix(rows, cols=0, bufferrows=1, buffercols=1,prefix="BM",directory=getwd())

Arguments

rows	Number of rows in the matrix
cols	Initial number of coulmns in the matrix
bufferrows	number of rows to be buffered if the row buffer is activated
buffercols	number of columns to be buffered
prefix	String to be used as start of name for any temporary files
directory	path to directory where temporary files should be stored

Author(s)

B. M. Bolstad <[email protected]>

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