import( BiocGenerics )
import( Biobase )
import( lattice )
importFrom( genefilter, rowVars )
importFrom( geneplotter, multiecdf )
importFrom( RColorBrewer, brewer.pal )

useDynLib( DESeq, calc_pvals )

exportClasses( "CountDataSet" )

exportMethods(
   counts, "counts<-",
   sizeFactors, "sizeFactors<-",
   conditions,  "conditions<-",
   dispTable, "dispTable",
   estimateSizeFactors,
   estimateDispersions
)

export(
   newCountDataSet,
   estimateVarianceFunctions,  # defunct
   varianceFitDiagnostics,     # defunct
   residualsEcdfPlot,          # defunct
   nbinomTest,
   getBaseMeansAndVariances,
   nbinomTestForMatrices,
   estimateSizeFactorsForMatrix,
   scvPlot,                    # defunct
   getVarianceStabilizedData,
   varianceStabilizingTransformation,
   makeExampleCountDataSet,
   adjustScvForBias,
   fitNbinomGLMsForMatrix,
   fitNbinomGLMs,
   nbkd.sf,
   nbinomGLMTest,
   dispTable,
   fitInfo,
   plotDispEsts,
   plotMA,
   plotPCA,
   newCountDataSetFromHTSeqCount
)
