checkSets: Check structure and retrieve sizes of a group of datasets.
In WGCNA: Weighted Correlation Network Analysis

checkSets

R Documentation

Check structure and retrieve sizes of a group of datasets.

Description

Checks whether given sets have the correct format and retrieves dimensions.

Usage

checkSets(data, checkStructure = FALSE, useSets = NULL)

Arguments

`data`	A vector of lists; in each list there must be a component named `data` whose content is a matrix or dataframe or array of dimension 2.
`checkStructure`	If `FALSE`, incorrect structure of `data` will trigger an error. If `TRUE`, an appropriate flag (see output) will be set to indicate whether `data` has correct structure.
`useSets`	Optional specification of entries of the vector `data` that are to be checked. Defaults to all components. This may be useful when `data` only contains information for some of the sets.

Details

For multiset calculations, many quantities (such as expression data, traits, module eigengenes etc) are presented by a common structure, a vector of lists (one list for each set) where each list has a component data that contains the actual (expression, trait, eigengene) data for the corresponding set in the form of a dataframe. This funtion checks whether data conforms to this convention and retrieves some basic dimension information (see output).

Value

A list with components

`nSets`	Number of sets (length of the vector `data`).
`nGenes`	Number of columns in the `data` components in the lists. This number must be the same for all sets.
`nSamples`	A vector of length `nSets` giving the number of rows in the `data` components.
`structureOK`	Only set if the argument `checkStructure` equals `TRUE`. The value is `TRUE` if the paramter `data` passes a few tests of its structure, and `FALSE` otherwise. The tests are not exhaustive and are meant to catch obvious user errors rather than be bulletproof.