WGCNA (version 1.43)

checkSets: 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.

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.

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).