#  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)
import(locfit)
importFrom("graphics", "abline", "axis", "curve", "grid", "legend",
           "lines", "mtext", "plot", "points", "smoothScatter")
importFrom("stats", "approxfun", "as.dist", "chisq.test", "cmdscale",
           "coefficients", "dbinom", "dnbinom", "dnorm", "fitted",
           "integrate", "lm.fit", "lm.wfit", "median", "model.matrix",
           "optim", "optimize", "p.adjust", "pbeta", "pbinom",
           "pchisq", "pf", "pgamma", "pnbinom", "pnorm", "predict",
           "pt", "qbeta", "qgamma", "qnorm", "qqnorm", "quantile",
           "rbinom", "rmultinom", "runif", "uniroot")
importFrom("utils", "read.delim", "read.table", "write.table")
if( tools:::.OStype() == "windows" ) importFrom("utils", "winMenuAddItem")

importFrom("limma",camera,contrastAsCoef,decideTests,fry,goana,kegga,is.fullrank,
     lmFit,loessFit,mroast,nonEstimable,plotMD,plotMDS,plotWithHighlights,removeExt,
     roast,romer,squeezeVar,subsetListOfArrays,zscoreGamma,zscoreT)
importClassesFrom("limma","LargeDataObject","Roast","MDS")

S3method(as.data.frame,TopTags)
S3method(as.matrix,DGEList)
S3method(aveLogCPM,default)
S3method(aveLogCPM,DGEList)
S3method(aveLogCPM,DGEGLM)
S3method(calcNormFactors,default)
S3method(calcNormFactors,DGEList)
S3method(camera,DGEList)
S3method(cpm,default)
S3method(cpm,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("dimnames<-",DGELRT)
S3method(equalizeLibSizes,default)
S3method(equalizeLibSizes,DGEList)
S3method(estimateCommonDisp,default)
S3method(estimateCommonDisp,DGEList)
S3method(estimateTrendedDisp,default)
S3method(estimateTrendedDisp,DGEList)
S3method(estimateTagwiseDisp,default)
S3method(estimateTagwiseDisp,DGEList)
S3method(estimateGLMCommonDisp,default)
S3method(estimateGLMCommonDisp,DGEList)
S3method(estimateGLMTrendedDisp,default)
S3method(estimateGLMTrendedDisp,DGEList)
S3method(estimateGLMTagwiseDisp,default)
S3method(estimateGLMTagwiseDisp,DGEList)
S3method(estimateDisp,default)
S3method(estimateDisp,DGEList)
S3method(fry,DGEList)
S3method(glmFit,default)
S3method(glmFit,DGEList)
S3method(glmQLFit,default)
S3method(glmQLFit,DGEList)
S3method(goana,DGEExact)
S3method(goana,DGELRT)
S3method(kegga,DGEExact)
S3method(kegga,DGELRT)
S3method(length,DGEList)
S3method(length,DGEExact)
S3method(length,TopTags)
S3method(length,DGEGLM)
S3method(length,DGELRT)
S3method(mroast,DGEList)
S3method(plotMD,DGEGLM)
S3method(plotMD,DGELRT)
S3method(plotMDS,DGEList)
S3method(predFC,default)
S3method(predFC,DGEList)
S3method(roast,DGEList)
S3method(romer,DGEList)
S3method(rpkm,default)
S3method(rpkm,DGEList)
S3method(splitIntoGroups,default)
S3method(splitIntoGroups,DGEList)
S3method(sumTechReps,default)
S3method(sumTechReps,DGEList)