GenomicSignatures-class
                        Virtual class inherited from
                        SummarizedExperiment
GenomicSignatures-methods
                        Methods and accesors for 'GenomicSignatures'
                        object
PCAGenomicSignatures    Construct 'PCAGenomicSignatures' object
PCAGenomicSignatures-class
                        PCAGenomicSignatures-class
PCAGenomicSignatures-methods
                        Methods and accesors for 'PCAGenomicSignatures'
                        object
PCinRAV                 Extract the list of PCs in a cluster
annotatePC              Annotate top PCs from the dataset
annotateRAV             Search the top enriched pathways for RAV
availableRAVmodel       List the available RAVmodels
buildAvgLoading         Calculate average loadings of each cluster
calculateScore          Calculate the validation score for a new
                        dataset
drawWordcloud           Draw wordcloud using the collection of RAVs'
                        MeSH terms
droplist                MeSH terms to be excluded in drawWordcloud
                        function
extractPC               PCA on gene expression profile
filterList              RAVs that will output with quality-control
                        messages
findKeywordInRAV        Find the rank of your keyword in the RAV's GSEA
                        annotation
findSignature           Find the RAVs with the keyword-containing
                        enriched pathways
findStudiesInCluster    Find the studies contributing each RAV
getModel                Download a PCAGenomicSignatures model
getRAVInfo              Extract information on a specific RAV
getStudyInfo            Extract information on a specific training
                        dataset
heatmapTable            Validation result in heatmap format
meshTable               Build a two-column word/frequency table
miniAllZ                Subset of allZ matrix constructed from 8 CRC
                        training datasets
miniRAVmodel            RAVmodel from 536 studies, annotated with
                        MSigDB C2
miniTCGA                Subset of TCGA-COAD and TCGA-BRCA RNA
                        sequencing datasets
plotAnnotatedPCA        Two-dimensional PCA plot with the PC annotation
plotValidate            Plot validation results in an interactive graph
res_hcut                Subset of allZ matrix constructed from 8 CRC
                        training datasets
rmNaInf                 Remove rows with missing and Inf values from a
                        matrix
sampleScoreHeatmap      Plot heatmap of the sample scores
subsetEnrichedPathways
                        Subset enriched pathways of RAV
validate                Validate new datasets
validatedSignatures     Validation result in data frame
