#  Calling the dynamic library.
useDynLib(edgeR, .registration=TRUE, .fixes=".c")

#  All functions exported other than those starting with "."
exportPattern("^[^\\.]")

exportClasses("DGEList","DGEExact","DGEGLM","DGELRT","TopTags")
exportMethods("show")

import(methods)
importFrom("limma",camera,goana,is.fullrank,loessFit,mroast,nonEstimable,plotMDS,roast,squeezeVar,subsetListOfArrays)
importClassesFrom("limma","LargeDataObject","Roast","MDS")

S3method(as.data.frame,TopTags)
S3method(as.matrix,DGEList)
S3method(calcNormFactors,default)
S3method(calcNormFactors,DGEList)
S3method(dim,DGEList)
S3method(dim,DGEExact)
S3method(dim,DGEGLM)
S3method(dim,DGELRT)
S3method(dim,TopTags)
S3method(dimnames,DGEList)
S3method(dimnames,DGEExact)
S3method(dimnames,DGEGLM)
S3method(dimnames,DGELRT)
S3method(dimnames,TopTags)
S3method("dimnames<-",DGEList)
S3method("dimnames<-",DGEGLM)
S3method(length,DGEList)
S3method(length,DGEExact)
S3method(length,TopTags)
S3method(length,DGEGLM)
S3method(length,DGELRT)
S3method(plotMDS,DGEList)
S3method(camera,DGEList)
S3method(roast,DGEList)
S3method(mroast,DGEList)
S3method(aveLogCPM,default)
S3method(aveLogCPM,DGEList)
S3method(aveLogCPM,DGEGLM)
S3method(cpm,DGEList)
S3method(estimateGLMCommonDisp,default)
S3method(estimateGLMCommonDisp,DGEList)
S3method(estimateGLMTrendedDisp,default)
S3method(estimateGLMTrendedDisp,DGEList)
S3method(estimateGLMTagwiseDisp,default)
S3method(estimateGLMTagwiseDisp,DGEList)
S3method(glmFit,default)
S3method(glmFit,DGEList)
S3method(predFC,default)
S3method(predFC,DGEList)
S3method(rpkm,default)
S3method(rpkm,DGEList)
S3method(sumTechReps,default)
S3method(sumTechReps,DGEList)
S3method(goana,DGEExact)
S3method(goana,DGELRT)
