import(methods)
import(ROC)
#import(DESeq)
import(edgeR)
import(samr)


# import methods from baySeq
importFrom(baySeq, getPriors.BB)
importFrom(baySeq, getLikelihoods.BB)
importFrom(baySeq, getPriors.NB)
importFrom(baySeq, getLikelihoods.NB)
importFrom(baySeq, topCounts)

# import methods from DESeq
importFrom(DESeq, newCountDataSet)
importFrom(DESeq, sizeFactors)
importFrom(DESeq, estimateDispersions)
importFrom(DESeq, estimateSizeFactors)
importFrom(DESeq, nbinomTest)
importFrom(DESeq, fitNbinomGLMs)
importFrom(DESeq, nbinomGLMTest)

# import methods from DESeq2
importFrom(DESeq2, DESeqDataSetFromMatrix)
importFrom(DESeq2, sizeFactors)
importFrom(DESeq2, estimateDispersions)
importFrom(DESeq2, nbinomWaldTest)
importFrom(DESeq2, nbinomLRT)
importFrom(DESeq2, results)



exportClasses(
    "TCC" 
)

export(
  show.TCC,
  names,
  length,
  "[",
  TCC,
  calcAUCValue,
  calcNormFactors,
  do_TbT,
  estimateDE,
  exactTestafterTbT,
  filterLowCountGenes,
  simulateReadCounts,
  getNormalizedData,
  getResult,
  MAplot,
  NBsample,
  plotFCPseudocolor,
  plot.TCC,
  WAD,
  ROKU,
  clusterSample
)

