
importFrom(stats, IQR)

importFrom(stats4, plot)

importFrom(BiocGenerics, NROW)

importFrom(snpStats, snp.rhs.tests, p.value, col.summary, snp.rhs.estimates)

importFrom(ff, ff, as.ram, ffrowapply, filename, is.open)

importFrom(bit, chunk)

importFrom(AnnotationDbi, get, mget, revmap, mappedkeys)

importMethodsFrom(IRanges, aggregate)

importFrom(IRanges, RangedData, IRanges)

importMethodsFrom(IRanges, elementMetadata, as.matrix, findOverlaps, "elementMetadata<-",
	as.data.frame, values, start, ranges)

importFrom(Biobase, featureNames, annotation, pData)

importMethodsFrom(GenomicRanges, seqnames)
importFrom(GenomicRanges, GRanges)

importFrom(Rsamtools, TabixFile)

importMethodsFrom(Rsamtools, scanTabix)

importClassFrom(GenomicRanges, GRanges)

importClassFrom(Rsamtools, TabixFile)

importFrom(VariantAnnotation, scanVcfHeader)

importClassFrom(IRanges, RangedData, DataTable, List, Vector, Annotated, 
	DataTableORNULL)

exportMethods("gwSnpTests", "show", "topFeats", "plot", transTab)

exportClasses("eqtlTestsManager", "eqtlEstimatesManager", "mcwBestCis",
   "gwSnpScreenResult", transManager, allSigCis, sensiCisInput,
   sensiCisOutput, mcwAllCis, cisRun, CisConfig)

export(gwSnpTests, topSnps, eqtlTests, topFeats, getCisMap, pData, plot,
	best.cis.eQTLs, chromsUsed, fullreport, 
	eqtlEstimates, probesManaged, snpsManaged,
	topScores, topGenes, locusNames, geneNames, geneIndcol, nthScores,
	vcf2sm, fdr, transScores, getBest, getAll, 
	getCall, transTab, meqtlTests, meta.best.cis.eQTLs, meta.All.cis.eQTLs,
	meta.transScores, annotation, sensanal, snplocsDefault, bindmaf,
	richNull, meta.bindmaf, meta.richNull, pifdr, 
 	All.cis, collectBest, 
        collectFiltered, cis.FDR.filter.SNPcentric, cis.FDR.filter.best)

export(best.trans.eQTLs, chrFilter, All.cis)


export("chrnames", "chrnames<-", "estimates", "estimates<-", 
"excludeRadius", "excludeRadius<-", "exFilter", "exFilter<-", 
"folderStem", "folderStem<-", "gchrpref", "gchrpref<-", "geneannopk", 
"geneannopk<-", "geneApply", "geneApply<-", "keepMapCache", "keepMapCache<-", 
"nperm", "nperm<-", "radius", 
"radius<-", "rhs", "rhs<-", "schrpref", "schrpref<-", 
"shortfac", "shortfac<-", "smchrpref", "smchrpref<-", 
"smFilter", "smFilter<-", "smpack", "smpack<-", "snpannopk", 
"snpannopk<-", "SSgen", "SSgen<-",
"cis.FDR.filter.SNPcentric.complete")

exportMethods("chrnames", "chrnames<-", "estimates", "estimates<-", 
"excludeRadius", "excludeRadius<-", "exFilter", "exFilter<-", 
"folderStem", "folderStem<-", "gchrpref", "gchrpref<-", "geneannopk", 
"geneannopk<-", "geneApply", "geneApply<-", "keepMapCache", "keepMapCache<-", 
"nperm", "nperm<-", "radius", 
"radius<-", "rhs", "rhs<-", "schrpref", "schrpref<-", 
"shortfac", "shortfac<-", "smchrpref", "smchrpref<-", 
"smFilter", "smFilter<-", "smpack", "smpack<-", "snpannopk", 
"snpannopk<-", "SSgen", "SSgen<-")
