importFrom("Biobase", "exprs")
importFrom("GGBase", "smList")
importFrom("AnnotationDbi", "get", "mget")
importFrom("ff", "ff", "ffrowapply", "[.ff", "filename", "as.ram")
importFrom("bit", "chunk")

importClassesFrom("Biobase", "eSet", "VersionedBiobase", "Versioned")
importClassesFrom("GGBase", "cnumOrMissing")
importClassesFrom("Rsamtools", "TabixFile")

importClassesFrom(IRanges, RangedData)
importFrom(IRanges, RangedData, space, findOverlaps)
importFrom(Rsamtools, yieldTabix, TabixFile, seqnamesTabix, scanTabix)

importFrom(stats,
           as.formula, formula, lm, resid)

exportMethods(gwSnpTests, topFeats, show, vcf2sm, probesManaged, snpsManaged)

export(eqtlTests, cisProxScores, clipPCs, pcChooser, permEx, makeDiagDirector,
	topFeats, vcf2sm, externalize, manhPlot, 
	interleave2cis, exome_minp, topSnps, checkCommonSNPs, makeCommonSNPs,
	relocate, transScores, mtransScores,
        sm2ped, mrefhap2sm, scoresByGenes, 
        dropMonomorphies, ieqtlTests, topScores,
	topGenes, locusNames, geneNames, geneIndcol,
	nthScores, eqtlEstimates, genewiseFDRtab, policywiseFDRtab,
	probeLocations, snpLocations, probeChromosomes, proximityList,
	transTab, tr1_perm, tr1_obs, restrictProbesToChrom,
	getGene2SnpList)


exportClass(eqtlTestsManager, multiCisDirector, cisProxScores, transManager,
	eqtlEstimatesManager, eqtlFDRtab)

