useDynLib(casper)

import(Biobase, EBarrays, IRanges, graphics, GenomicRanges, methods)
importFrom(BiocGenerics, strand, "strand<-")
importFrom(gaga, fitNNSingleHyp, getpar)
importFrom(GenomeInfoDb, seqlengths)
importFrom(GenomicFeatures, transcripts, exonsBy, makeTranscriptDb)
importClassesFrom(GenomicFeatures, TxDb)
importFrom(gtools, rdirichlet)
importFrom(limma, lmFit, contrasts.fit, treat)
importFrom(mgcv,gam,predict.gam,s)
importMethodsFrom(Rsamtools, scanBam, scanBamHeader, ScanBamParam)
importFrom(Rsamtools, scanBamFlag)
importFrom(rtracklayer, import)
importFrom(S4Vectors, Rle, DataFrame, isSingleStringOrNA, isTRUEorFALSE)
importFrom(sqldf, sqldf)
importFrom(survival,Surv,survfit)
importMethodsFrom(VGAM, Coef, model.matrix, predict)
importFrom(VGAM,vglm,betabinomial)

#export regular functions
export(asymmetryCheck, calcDenovo, calcExp, casperDesign, createDenovoGenome, denovoExpr, getDistrs, getIsland, genePlot, getRoc, mergeBatches, mergeExp, modelPrior, pathCounts, plotPriorAS, posprob, probNonEquiv, procBam, procGenome, pvalTreat, qqnormGenomeWide, quantileNorm, relativeExpr, relexprByGene, rmShortInserts, simMAE, simMultSamples, simReads, transcripts, variants, "variants<-", getReads, getNreads, getChr, getIsland, subsetGenome, txLength, wrapKnown, simMAE, simMAEcheck)

exportClasses(annotatedGenome, simulatedSamples, pathCounts, procBam)
#export general methods
exportMethods("plot","lines","coef","[","[[","as.list")

