
# IMPORT PHASE

#Generated by codetoolsBioC version 0.0.16
#Timestamp: Thu Dec 15 21:13:25 2011

#Imports: AnnotationDbi, Biobase, BiocGenerics, bit, ff, GenomicRanges,
#         GGBase, graphics, IRanges, Matrix, methods, Rsamtools,
#         snpStats, stats, utils

importClassesFrom(GenomicRanges, GRanges)

importClassesFrom(GGBase, cnumOrMissing, cwSnpScreenResult, genesym,
                  gwSnpScreenResult, probeId, rsid, smlSet, snpdepth)

importClassesFrom(IRanges, RangedData)

importClassesFrom(methods, ANY, call, character, environment,
                  envRefClass, formula, integer, list, logical,
                  missing, numeric)

importClassesFrom(Rsamtools, TabixFile)

importMethodsFrom(AnnotationDbi, as.list, colnames, get, mappedkeys,
                  mget, ncol, nrow, revmap, sample, summary)

importMethodsFrom(Biobase, annotation, featureNames, pData,
                  "pData<-", sampleNames)

importMethodsFrom(BiocGenerics, cbind, duplicated, eval, intersect,
                  lapply, order, paste, pmax, pmin, rbind, sapply,
                  union, unique)

importMethodsFrom(GenomicRanges, seqlengths, seqlevels, "seqlevels<-",
                  seqnames, strand, "strand<-")

importMethodsFrom(GGBase, chrnum, probeId, rsid, smList, snps, exprs)

importMethodsFrom(IRanges, "colnames<-", diff, elementLengths,
                  elementMetadata, "elementMetadata<-", end, "end<-",
                  findOverlaps, gsub, ifelse, "%in%", match, matchMatrix,
                  mean, na.omit, punion, quantile, ranges, "ranges<-",
                  reduce, Rle, rownames, "rownames<-", runValue, shift,
                  sort, split, start, "start<-", t, unlist, values,
                  "values<-", which, which.max)

importMethodsFrom(Matrix, all.equal, diag, format, print, unname)

importMethodsFrom(methods, coerce, show)

importMethodsFrom(Rsamtools, scanTabix, seqnamesTabix, yieldTabix)

importMethodsFrom(snpStats, p.value)

importFrom(Biobase, assayDataNew, selectSome)

importFrom(bit, chunk)

importFrom(limma, lmFit)

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

importFrom(GenomicRanges, GRanges)

importFrom(GGBase, getSS, exprs)

importFrom(graphics, axis, smoothScatter)

importFrom(IRanges, DataFrame, IRanges, IRangesList, RangedData)

importFrom(methods, "@<-", as, callGeneric, is, new, validObject)

importFrom(snpStats, col.summary, read.snps.long, snp.rhs.estimates,
           snp.rhs.tests)

importFrom(stats, as.formula, coef, formula, lm, pchisq, qchisq,
           rchisq, resid, rnorm)

importFrom(utils, packageVersion, sessionInfo, write.table)

# end generated

# EXPORT PHASE

exportMethods(gwSnpTests, topSnps, topFeats, show, vcf2sm, 
   probesManaged, snpsManaged, c, fullreport)

#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, geneRanges, best.cis.eQTLs)
#

export(eqtlTests, clipPCs, permEx, externalize,
	manhPlot, transScores, dropMonomorphies, eqtlEstimates,
	transTab, best.cis.eQTLs, getGene2SnpList, makeGRanges,
	makeCommonSNPs, checkCommonSNPs,
# some of the following are general infrastructure and should move
	probeLocations, probeChromosomes, probeSequences,
	snpLocations, proximityList, getGene2SnpList, restrictProbesToChrom,
	regressOut, all.cis.eQTLs)


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

exportClass(eqtlEstimatesManager, eqtlTestsManager,
	transManager, eqtlFDRtab, eqtlFDRSummary)

