.calculateSilhouetteWidth	dot-calculateSilhouetteWidth
.loadingCor	dot-loadingCor
.PCAGenomicSignatures	PCAGenomicSignatures-class
.RAVName	dot-RAVName
annotatePC	annotatePC
annotateRAV	annotateRAV
buildAvgLoading	buildAvgLoading
calculateScore	calculateScore
colData	GenomicSignatures-methods
drawWordcloud	drawWordcloud
droplist	droplist
extractPC	extractPC
findKeywordInRAV	findKeywordInRAV
findSignature	findSignature
findStudiesInCluster	findStudiesInCluster
geneSets	GenomicSignatures-methods
geneSets,GenomicSignatures-method	GenomicSignatures-methods
geneSets<-	GenomicSignatures-methods
geneSets<-,GenomicSignatures-method	GenomicSignatures-methods
GenomicSignatures-class	GenomicSignatures-class
GenomicSignatures-methods	GenomicSignatures-methods
getModel	getModel
gsea	PCAGenomicSignatures-methods
gsea,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
gsea<-	PCAGenomicSignatures-methods
gsea<-,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
heatmapTable	heatmapTable
makeGeneList	makeGeneList
mesh	PCAGenomicSignatures-methods
mesh,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
mesh<-	PCAGenomicSignatures-methods
mesh<-,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
meshTable	meshTable
metadata	GenomicSignatures-methods
miniAllZ	miniAllZ
miniRAVmodel	miniRAVmodel
miniTCGA	miniTCGA
msigdb_gsea	msigdb_gsea
PCAGenomicSignatures	PCAGenomicSignatures
PCAGenomicSignatures-class	PCAGenomicSignatures-class
PCAGenomicSignatures-methods	PCAGenomicSignatures-methods
PCAsummary	PCAGenomicSignatures-methods
PCAsummary,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
PCAsummary<-	PCAGenomicSignatures-methods
PCAsummary<-,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
PCinRAV	PCinRAV
plotAnnotatedPCA	plotAnnotatedPCA
plotValidate	plotValidate
RAVindex	GenomicSignatures-methods
RAVindex,GenomicSignatures-method	GenomicSignatures-methods
res_hcut	res_hcut
rmNaInf	rmNaInf
rowNorm	rowNorm
run_gsea	run_gsea
sampleScoreHeatmap	sampleScoreHeatmap
show,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
silhouetteWidth	PCAGenomicSignatures-methods
silhouetteWidth,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
silhouetteWidth<-	PCAGenomicSignatures-methods
silhouetteWidth<-,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
studies	PCAGenomicSignatures-methods
studies,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
studies<-	PCAGenomicSignatures-methods
studies<-,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
subsetEnrichedPathways	subsetEnrichedPathways
subsetGSEA	subsetGSEA
trainingData	PCAGenomicSignatures-methods
trainingData,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
trainingData<-	PCAGenomicSignatures-methods
trainingData<-,PCAGenomicSignatures-method	PCAGenomicSignatures-methods
updateNote	GenomicSignatures-methods
updateNote,GenomicSignatures-method	GenomicSignatures-methods
updateNote<-	GenomicSignatures-methods
updateNote<-,GenomicSignatures-method	GenomicSignatures-methods
validate	validate
validatedSignatures	validatedSignatures
