import(methods)

importClassesFrom(Biobase, ExpressionSet)
importMethodsFrom(Biobase, exprs, pData)

importFrom(graphics, abline, layout, legend, par, plot, points, rect, text)
importFrom(grDevices, dev.interactive, terrain.colors)

importFrom(stats, cor, hclust, heatmap, IQR, lowess, mad, median,
           model.matrix, pf, pnorm, psignrank, pwilcox, quantile,
           rnorm, sd, var)

importFrom(samr,samr)
useDynLib(GeneSelector)

exportClasses("GeneRanking", "FoldMatrix", "BootMatrix", "RepeatedRanking",
              "StabilityOverlap", "StabilityDistance", "StabilityUnion", 
              "AggregatedRanking", "GeneSelectorOutput")


exportMethods("show", "summary", "toplist", "plot", "SelectedGenes", 
              "RankingBaldiLong",
              "RankingEbam", "RankingFC", "RankingFoxDimmic", "RankingLimma", "RankingPermutation",
              "RankingSam", "RankingShrinkageT", "RankingSoftthresholdT",
              "RankingTstat", "RankingWelchT", "RankingWilcEbam", "RankingWilcoxon",
              "GenerateFoldMatrix", "GenerateBootMatrix",
              "RepeatRanking", "GetStabilityOverlap", "GetStabilityDistance", "GetStabilityUnion", 
              "AggregateSimple", "AggregatePenalty", "AggregateMC", "AggregateSVD", "GeneSelector",
              "HeatmapRankings", "MergeRankings", "MergeMethods", "dispersion")

export("samplingcontrol")





