useDynLib("XDE")
import(Biobase, methods)
#MergeMaid.  Can not import all of MergeMaid b/c of conflicts with graphics
##importClassesFrom("MergeMaid", "mergeExpressionSet", "mergeCor", "mergeCoeff")
##importMethodsFrom("MergeMaid", geneStudy, "geneStudy<-", exprs, integrative.cors, intCor, intcorDens)
##importFrom("MergeMaid", mergeExprs)
importClassesFrom("MergeMaid", mergeExpressionSet)
importMethodsFrom("MergeMaid", intCor, intcorDens, pairwise.cors)
importMethodsFrom("genefilter", rowttests)
importFrom("genefilter", rowSds, rowVars)
importFrom("gtools", permute)
importFrom("graphics", legend, pairs, par, plot, smoothScatter)
importFrom("grDevices", colorRampPalette)
importFrom("stats", as.ts, cor, median, princomp, quantile, rnorm, runif,
           var)
importFrom("utils", str)
exportClasses("ExpressionSetList", "XdeParameter", "XdeMcmc")
exportMethods("[", "[[", "$",
              bayesianEffectSize,
              "bayesianEffectSize<-",
              burnin,
              "burnin<-",
              calculateBayesianEffectSize,
              firstMcmc,
              "firstMcmc<-",
              coerce,
	      dim,
              directory,
              "directory<-",
              featureData,              
              featureNames,
              geneCenter,
##	      goodnessOfFit,	      
              hyperparameters,
              "hyperparameters<-",
              initialize,
             iterations,
              "iterations<-",
	      lapply,
              lastMcmc,
              "lastMcmc<-",
              notes,
              nrow,
              nSamples,
              output,
              "output<-",
              pData,
              phenotypeLabel,
              "phenotypeLabel<-",
              plot,
              posteriorAvg,
	      "posteriorAvg<-",
              savedIterations,
              seed,
	      "seed<-",
              show,
              showIterations,
              "showIterations<-",
              .standardizedDelta,
              standardizeSamples,
              studyCenter,
              studyNames,
              "studyNames<-",
              thin,
              "thin<-",
              tuning,
              "tuning<-",
              updates,
              "updates<-",
              zeroNu)
export(calculatePosteriorAvg,
       empiricalStart,
       ssStatistic,
       symbolsInteresting,
       xde,
       xsScores)

#export(.goodnessOfFit, computeGOF)







              
              
              

              
              
