.DollarNames.FactorisedExperiment
                        Command line completion for '$'
FactorisedExperiment-class
                        FactorisedExperiment: A container for the
                        results of factor analysis
ModularExperiment-class
                        ModularExperiment: A container for the results
                        of module analysis
ReducedExperiment-class
                        ReducedExperiment: A container for
                        dimensionally-reduced representations
[,FactorisedExperiment,ANY,ANY,ANY-method
                        Extract and replace parts of ReducedExperiment
                        objects
assessSoftThreshold     Assess soft thresholding power for WGCNA
assignments             Get and set module feature assignments
associateComponents     Runs linear models for components and
                        sample-level data
calcEigengenes          Calculate eigengenes for new data
cbind,FactorisedExperiment-method
                        Combine ReducedExperiment objects by columns or
                        rows
componentNames<-,FactorisedExperiment-method
                        Get names of dimensionally-reduced components
dendrogram              Get the dendrogram stored in a
                        ModularExperiment
dim,ReducedExperiment-method
                        Get the dimensions of a Reducedexperiment
                        object
estimateFactors         Perform dimensionality reduction using
                        Independent Component Analysis
estimateStability       Estimate stability of factors as a function of
                        the number of components
getAlignedFeatures      Get feature alignments with factors
getCentrality           Get correlation of features with module
                        eigengenes
getCommonFeatures       Get common factor features
getGeneIDs              Gets alternative gene annotations from biomaRt
getMsigdbT2G            Get TERM2GENE dataframe from MSigDB
identifyModules         Apply dimensionality reduction using Weighted
                        Gene Correlation Network Analysis
loadings,FactorisedExperiment-method
                        Get and set loadings
modulePreservation      Get module preservation statistics
nModules,ModularExperiment-method
                        Prints individual lengths of samples,
                        components and features
names<-,FactorisedExperiment-method
                        Get feature names
plotCommonFeatures      Heatmap comparing commonality across factors
plotDendro              Plot a dendrogram stored in a ModularExperiment
plotModulePreservation
                        Plot module preservation statistics
plotStability           Plot component stability as a function of the
                        number of components
projectData             Project new data using pre-defined factors
reduced                 Get and set reduced data
runEnrich               Functional enrichment analyses for
                        dimensionally-reduced data
runICA                  Run standard or stabilised Independent
                        Component Analysis
runWGCNA                Run WGCNA for a data matrix
sampleNames             Get sample names
show                    Prints a summary of a ReducedExperiment object
stability               Get and setting the stability values for
                        factors
