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")
: returnsTRUE
if the row buffer is active andFALSE
otherwise.- is.ColMode
signature(object = "BufferedMatrix")
: returnsTRUE
if the row buffer is inactive andFALSE
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 Rmatrix
- 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 objectas(matrix,BufferedMatrix)
:Coerce
matrix
toBufferedMatrix
.as(BufferedMatrix,matrix)
:Coerce the
Buffered
tomatrix
.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