
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)

export(gwSnpTests, topSnps, eqtlTests, topFeats, getCisMap, pData, plot,
	best.cis.eQTLs, chromsUsed, fullreport, 
	eqtlEstimates, probesManaged, snpsManaged,
	topScores, topGenes, locusNames, geneNames, geneIndcol, nthScores,
	vcf2sm, All.cis.eQTLs, fdr, transScores, getBest, getAll, 
	getCall, transTab, meqtlTests, meta.best.cis.eQTLs, meta.All.cis.eQTLs,
	meta.transScores, annotation)

export(best.trans.eQTLs)
