importFrom(BiocGenerics, annotation, "annotation<-")
import(isa2)
import(Category)
import(AnnotationDbi)
import(Biobase)
import(genefilter)
import(methods)
import(DBI)

export(ISA, ISANormalize, ISAIterate, ISAUnique, ISASweep,
       ISASweepGraph, ISASweepGraphPlot, ISARobustness, ISAFilterRobust)

export(ISAEnrichment, ISAGO, ISAKEGG, ISACHR, ISAmiRNA)#, ISA.DBD)

export(gograph, gographPlot, expPlotCreate, expPlotColbar,
       expPlot, condPlot, overlap, overlapPlot, mnplot, ISAmnplot,
       ISA2heatmap, profilePlot)
       
export(ISAHTMLTable, ISAHTMLModules, ISAHTML)

exportMethods("featExprs", "sampExprs",
              "prenormalized", "prenormalized<-",
              "hasNA", "hasNA<-")

S3method(print, ISAexpPlot)

exportMethods("seedData", "runData",
              "getFeatures", "getSamples",
              "getFeatureNames", "getSampleNames",
              "getFeatureMatrix", "getSampleMatrix",
              "getFullFeatureMatrix", "getFullSampleMatrix",
              "getFeatureScores", "getSampleScores",
              "getNoFeatures", "getNoSamples",
              "featureThreshold", "sampleThreshold",
              "getOrganism")

exportMethods("makeValidParams", "ontology", "ontology<-", "conditional",
              "conditional<-", "drive", "drive<-", "hyperGTest")

exportMethods("summary", "htmlReport", "pvalues", "geneCounts",
              "oddsRatios", "expectedCounts", "universeCounts",
              "universeMappedCount", "geneMappedCount", "geneIdUniverse",
              "geneIdsByCategory", "sigCategories")

exportMethods("coerce")

export("annotate")
