WGCNA: BD.getData – R documentation

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BD.getData

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