Function reference • GenomicSuperignature

Classes Exported classes
`GenomicSignatures-class`	Virtual class inherited from SummarizedExperiment
`PCAGenomicSignatures-class` `.PCAGenomicSignatures`	PCAGenomicSignatures-class
Constructors Build objects with designated constructor functions
`PCAGenomicSignatures()`	Construct `PCAGenomicSignatures` object
Methods and Accessors Discover content within PCAGenomicSignatures
`RAVindex(<GenomicSignatures>)` `geneSets(<GenomicSignatures>)` `updateNote(<GenomicSignatures>)` `version(<GenomicSignatures>)` `geneSets<-`(<GenomicSignatures>) `updateNote<-`(<GenomicSignatures>)	Methods and accesors for `GenomicSignatures` object
`studies<-`(<PCAGenomicSignatures>) `silhouetteWidth<-`(<PCAGenomicSignatures>) `gsea<-`(<PCAGenomicSignatures>) `trainingData<-`(<PCAGenomicSignatures>) `mesh<-`(<PCAGenomicSignatures>) `PCAsummary<-`(<PCAGenomicSignatures>) `studies(<PCAGenomicSignatures>)` `silhouetteWidth(<PCAGenomicSignatures>)` `gsea(<PCAGenomicSignatures>)` `trainingData(<PCAGenomicSignatures>)` `mesh(<PCAGenomicSignatures>)` `PCAsummary(<PCAGenomicSignatures>)` `show(<PCAGenomicSignatures>)`	Methods and accesors for `PCAGenomicSignatures` object
Model Building Functions for PCAGenomicSignatures model building
`buildAvgLoading()`	Calculate average loadings of each cluster
`findStudiesInCluster()`	Find the studies contributing each RAV
`PCinRAV()`	Extract the list of PCs in a cluster
`rmNaInf()`	Remove rows with missing and Inf values from a matrix
Model Application Functions for applying PCAGenomicSignatures model to a new data
`calculateScore()`	Calculate the validation score for a new dataset
`getModel()`	Download a PCAGenomicSignatures model
`validate()`	Validate new datasets
Extract Output and Metadata
`annotatePC()`	Annotate top PCs from the dataset
`annotateRAV()`	Search the top enriched pathways for RAV
`availableRAVmodel()`	List the available RAVmodels
`extractPC()`	PCA on gene expression profile
`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
`getRAVInfo()`	Extract information on a specific RAV
`getStudyInfo()`	Extract information on a specific training dataset
`meshTable()`	Build a two-column word/frequency table
`subsetEnrichedPathways()`	Subset enriched pathways of RAV
`validatedSignatures()`	Validation result in data frame
Visualization
`drawWordcloud()`	Draw wordcloud using the collection of RAVs' MeSH terms
`heatmapTable()`	Validation result in heatmap format
`plotAnnotatedPCA()`	Two-dimensional PCA plot with the PC annotation
`plotValidate()`	Plot validation results in an interactive graph
`sampleScoreHeatmap()`	Plot heatmap of the sample scores
Misc. Package Docs Other package information and data
`droplist`	MeSH terms to be excluded in drawWordcloud function
`filterList`	RAVs that will output with quality-control messages
`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
`res_hcut`	Subset of allZ matrix constructed from 8 CRC training datasets

Reference

Classes

Constructors

Methods and Accessors

Model Building

Model Application

Extract Output and Metadata

Visualization

Misc. Package Docs