BD.getData {WGCNA}

Various basic operations on BlockwiseData objects.

Description

These functions implement basic operations on BlockwiseData objects. Blockwise here means that the data is too large to be loaded or processed in one piece and is therefore split into blocks that can be handled one by one in a divide-and-conquer manner.

Usage

BD.actualFileNames(bwData)
BD.nBlocks(bwData)
BD.blockLengths(bwData)
BD.getMetaData(bwData, blocks = NULL, simplify = TRUE)
BD.getData(bwData, blocks = NULL, simplify = TRUE)
BD.checkAndDeleteFiles(bwData)

Arguments

bwData

A BlockwiseData object.

blocks

Optional vector of integers specifying the blocks on which to execute the operation.

simplify

Logical: if the blocks argument above is of length 1, should the returned list be simplified by removing the redundant outer list structure?

Details

Several functions in this package use the concept of blockwise, or "divide-and-conquer", analysis. The BlockwiseData class is meant to hold the blockwise data, or all necessary information about blockwise data that is saved in disk files.

Value

BD.actualFileNames

returns a vector of character strings giving the file names in which the files are saved, or NULL if the data are held in-memory.

BD.nBlocks

returns the number of blocks in the input object.

BD.blockLengths

returns the block lengths (results of applying length to the data in each block).

BD.getMetaData

returns a list with one component per block. Each component is in turn a list containing the stored meta-data for the corresponding block. If blocks is of length 1 and simplify is TRUE, the outer (redundant) list is removed.

BD.getData

returns a list with one component per block. Each component is in turn a list containing the stored data for the corresponding block. If blocks is of length 1 and simplify is TRUE, the outer (redundant) list is removed.

BD.checkAndDeleteFiles

deletes the files referenced in the input bwData if they exist.

Warning

The definition of BlockwiseData and the functions here should be considered experimental and may change in the future.

Author(s)

Peter Langfelder

See Also

Definition of and other functions on BlockwiseData:

newBlockwiseData for creating new BlockwiseData objects;

mergeBlockwiseData for merging blockwise data structure;

addBlockToBlockwiseData for adding a new block to existing blockwise data;