useDynLib("XDE")
import(Biobase, methods, stats, graphics)
##import(Biobase, coda, methods, graphics, stats)
#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)
##importFrom("multtest", mt.teststat)
exportClasses("ExpressionSetList", "XdeParameter", "XdeMcmc")
exportMethods("[", "[[", "$",
              bayesianEffectSize,
              "bayesianEffectSize<-",
              burnin,
              "burnin<-",
              calculateBayesianEffectSize,
              firstMcmc,
              "firstMcmc<-",
              coerce,
              directory,
              "directory<-",
              featureData,              
              featureNames,
              geneCenter,
              hyperparameters,
              "hyperparameters<-",
              initialize,
              .integrativeCorrelationFilter,
              iterations,
              "iterations<-",
	      xapply,
              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 when debugging
##exportMethods(.pca, .studySplit)
##export(.integ.norm,
##       .integ.cal,
##       .chainInitialize,
##       .hyperparametersDefault,
##       .outputDefault,
##       .parameterNames,
##       .permuteClassLabels,
##       .permutePhenotype,
##       .tuningDefault,
##       .updatesDefault,
##       .xdeparameterList)






              
              
              

              
              
