# 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