WGCNA: newBlockwiseData – R documentation

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newBlockwiseData

Create, merge and expand BlockwiseData objects

Description

These functions create, merge and expand BlockwiseData objects for holding in-memory or disk-backed blockwise data. 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

newBlockwiseData(
   data, 
   external = FALSE, 
   fileNames = NULL, 
   doSave = external, 
   recordAttributes = TRUE, 
   metaData = list())

mergeBlockwiseData(...)

addBlockToBlockwiseData(
   bwData,
   blockData,
   external = bwData$external,
   blockFile = NULL,
   doSave = external,
   recordAttributes = !is.null(bwData$attributes),
   metaData = NULL)

Arguments

`data`	A list in which each component carries the data of a single block.
`external`	Logical: should the data be disk-backed (`TRUE`) or in-memory (`FALSE`)?
`fileNames`	When `external` is `TRUE`, this argument must be a character vector of the same length as `data`, giving the file names for the data to be saved to, or where the data is already located.
`doSave`	Logical: should data be saved? If this is `FALSE`, it is the user's responsibility to ensure the files supplied in `fileNames` already exist and contain the expected data.
`recordAttributes`	Logical: should `attributes` of the given data be recorded within the object?
`metaData`	A list giving any additional meta-data for `data` that should be attached to the object.
`bwData`	An existing `BlockwiseData` object.
`blockData`	A vector, matrix or array carrying the data of a single block.
`blockFile`	File name where data contained in `blockData` should be saved.
`...`	One or more objects of class `BlockwiseData`.

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.

The data can be stored in disk files (one file per block) or in-memory. In memory storage is provided so that same code can be used for both smaller (single-block) data where disk storage could slow down operations as well as larger data sets where disk storage and block by block analysis are necessary.

Value

All three functions return a list with the class set to "BlockwiseData", containing the following components:

`external`	Copy of the input argument `external`
`data`	If `external` is `TRUE`, an empty list, otherwise a copy of the input `data`.
`fileNames`	Copy of the input argument `fileNames`.
`lengths`	A vector of lengths (results of `length`) of elements of `data`.
`attributes`	If input `recordAttributes` is `TRUE`, a list with one component per block (component of `data`); each component is in turn a list of attributes of that component of `data`.
`metaData`	A copy of the input `metaData`.

Warning

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

Author(s)

Peter Langfelder