NAMESPACE

# Generated by roxygen2: do not edit by hand

export(BBI)
export(LDLT)
export(MIMQTL)
export(SIMQTL)
export(adjustPvaluesSidak)
export(adjustThreshBonf)
export(adjustThreshGalwey)
export(adjustThreshSidak)
export(aireml)
export(allPairAligns)
export(barplotGeneticMap)
export(barplotInsertSizes)
export(barplotReadCounts)
export(betterSummary)
export(binaryClassif)
export(blast2granges)
export(boxplotCandidateQtl)
export(calcAsymptoticBayesFactorWakefield)
export(calcAvgPwDiffBtwHaplos)
export(calcExactBayesFactorServinStephens)
export(calcFreqMissSnpGenosPerGeno)
export(calcFreqMissSnpGenosPerSnp)
export(calcFreqNaVcf)
export(calcL10ApproximateBayesFactorWen)
export(calcL10ApproximateBayesFactorWenStephens)
export(caretFitBglr)
export(caretFitQtl)
export(caretFitRrblup)
export(caretFitVarbvs)
export(caretGridBglr)
export(caretGridQtl)
export(caretGridRrblup)
export(caretGridVarbvs)
export(caretPredictBglr)
export(caretPredictQtl)
export(caretPredictRrblup)
export(caretPredictVarbvs)
export(caretSummary)
export(chiSqSnpGenos)
export(chromNames2integers)
export(closeCarthagene)
export(clusteredness)
export(coancestry2relmat)
export(confidenceGenoOneVar)
export(controlBayesFdr)
export(convertFactorColumnsToCharacter)
export(convertImputedTo012)
export(convertVcfToGenoDoseWithBcftools)
export(cor2cov)
export(corrMatAR1)
export(correctSpatialHeterogeneity)
export(correspondenceJoinMap2qtl)
export(countGenotypicClasses)
export(covMatAR1)
export(coverageBams)
export(coverageRegions)
export(createA)
export(defLinkgroupsWithCarthagene)
export(depthsPerRegion)
export(depthsPerSample)
export(descPlate)
export(df2gr)
export(dimVcf)
export(discardMarkersMissGenos)
export(discardSnpsLowMaf)
export(distConsecutiveSnps)
export(distSnpPairs)
export(drawLocCrossovers)
export(dsVcf2dose)
export(effNbIndepTests)
export(effNbIndepTestsPerChr)
export(em_solve)
export(emptyWells)
export(emreml)
export(estMrkOrderGenDistsWithCarthagene)
export(estimGenRel)
export(estimH2means)
export(estimLd)
export(estimLdPerChr)
export(estimSnpAf)
export(estimSnpMaf)
export(estimatePi0WithEbf)
export(estimatePi0WithQbf)
export(extractFasta)
export(fecundation)
export(filterSegreg)
export(filterVariantCalls)
export(fitPhyDistVsLd)
export(formatReadCountsPerLane)
export(freadBedtoolsCoverageHist)
export(gcContent)
export(gemma)
export(gemmaUlmmPerChr)
export(genoAr1Coef)
export(genoClasses2JoinMap)
export(genoClasses2genoDoses)
export(genoDoses2ASMap)
export(genoDoses2Vcf)
export(genoDoses2bimbam)
export(genoDoses2genoClasses)
export(genomicControl)
export(getBreedingGameConstants)
export(getBreedingGameSetup)
export(getEllipsisCoords)
export(getHaplosInd)
export(getHaplosInds)
export(getIndNamesFromHaplos)
export(getJoinMapSegregs)
export(getMeanVarBetaDist)
export(getNbPCsMinimAvgSqPartCor)
export(getParamsBetaDist)
export(getSamplesFromVcfFile)
export(getSparseInv)
export(getSsrGenosFromPlantGrapePdf)
export(gibbsJanss2012)
export(gps2kml)
export(grSummaryPerBin)
export(gtVcf2dose)
export(gtVcf2genoClasses)
export(h2v1WX2019)
export(h2v2WX2019)
export(haplosAlleles2num)
export(haplosList2Matrix)
export(hinton)
export(imageMat)
export(imageWithScale)
export(imputeGenosWithMean)
export(imputeGenosWithMeanPerPop)
export(indexGenoDoses)
export(indexVcfFile)
export(infoGeneticMap)
export(infoVariantCalls)
export(initPlates)
export(inlaAM)
export(inlineFctForm)
export(invertGRanges)
export(isSingular)
export(jagsAM)
export(jagsAMmv)
export(joinMap2backcross)
export(joinMap2designMatrix)
export(lengthenPlate)
export(lmerAM)
export(loadBlast)
export(loadMummer)
export(loadPlates)
export(loadReadCountsPerIndAndLane)
export(lodLinkage)
export(log10WeightedSum)
export(mae)
export(maf2genoFreq)
export(makeCross)
export(makeCrosses)
export(makeDfInitPhenos)
export(makeDfPhenos)
export(makeExampleDataFile)
export(makeExamplePlantFile)
export(makeGameteSingleInd)
export(makeGameteSingleIndSingleChrom)
export(makeGridWenStephens)
export(makeMmeElements)
export(makeMmeLhs)
export(makeMmeRhs)
export(matWide2Long)
export(matrixTrace)
export(mbe)
export(mergeOverlaps)
export(mpInv)
export(msd)
export(mummer2granges)
export(n0WX2019)
export(openCarthagene)
export(orthoRotate2D)
export(overlayBarplots)
export(parseCgGroup)
export(parseCgHeaprint)
export(parseCgMaprintd)
export(parseCgMrkinfo)
export(parseCgPwMatrix)
export(pca)
export(permuteAllelesInGenosDose)
export(permuteAllelesInHaplosNum)
export(phasedJoinMapCP2qtl)
export(plantTrialLmmFitCompSel)
export(plotAligns)
export(plotEllipsis)
export(plotFalconer)
export(plotGRanges)
export(plotGridMissGenos)
export(plotHaplosMatrix)
export(plotHistAllelFreq)
export(plotHistMinAllelFreq)
export(plotHistPval)
export(plotInfoVariantCalls)
export(plotLd)
export(plotLdSry)
export(plotMapSxGDomaineChapitre)
export(plotMcmcChain)
export(plotPca)
export(plotPedigree)
export(plotPhyDistVsLdSry)
export(plotPhyVsGenDistances)
export(plotPlate)
export(plotResidualsBtwYears)
export(plotTukey)
export(plotVcfPercNa)
export(plotWithScale)
export(pooledVar)
export(powerWX2019)
export(precMatAR1)
export(prettyPrintBetterSummary)
export(pruneSnpsLd)
export(pseudoR2)
export(pve2beta)
export(qqplotPval)
export(qtlrelPerChr)
export(quantNorm)
export(quantilesBinnedSnpData)
export(quass)
export(randPlate)
export(readBcftoolsCounts)
export(readBiomercator)
export(readGenoDoseFileFromBcftools)
export(readGenosFastphase)
export(readGenosFimpute)
export(readGenosFindhap)
export(readHaplosFastphase)
export(readOutSTRUCTURE)
export(readOutputsFimpute)
export(readOutputsFindhap)
export(readPlinkMendel)
export(readSamDict)
export(readSegregJoinMap)
export(readVcfSubset)
export(rearrangeInputsForAssoGenet)
export(recodeGenosMinorSnpAllele)
export(recodeIntoDominant)
export(reformatGenoClasses)
export(regplot)
export(removeFileExtension)
export(renameVcfSamples)
export(requireNamespaces)
export(rhoWX2019)
export(rmatnorm)
export(rmse)
export(rmsre)
export(rngVcf2df)
export(rrmse)
export(runCarthagene)
export(runFastphase)
export(runFimpute)
export(runFindhap)
export(sampleWX2019)
export(segSites2allDoses)
export(segSites2snpCoords)
export(seqIdStartEnd2GRanges)
export(setGt2Na)
export(setJoinMapPhasesFromParentalLinkGroups)
export(setupQtlCrossObject)
export(significantTests)
export(simulAnimalModel)
export(simulAr1Ar1)
export(simulBslmm)
export(simulBvsr)
export(simulCoalescent)
export(simulGeneralisedLogistic)
export(simulGenosDose)
export(simulGenosDoseStruct)
export(simulLogistic)
export(simulRefAltSnpAlleles)
export(simulRefseqCompatibleWithVcf)
export(simulSnpEffectsTraits12)
export(simulTrait3)
export(simulTraits12)
export(snpCoordsDf2Gr)
export(solveMme)
export(sortVcfFile)
export(splitGenomesTrainTest)
export(stanAM)
export(stanAMmv)
export(stanAMmvwriteModel)
export(stanAMwriteModel)
export(statsAllPairAligns)
export(statsStrongAssign)
export(stopIfNotValidGenosDose)
export(stopIfNotValidHaplos)
export(structure2clumpp)
export(subsetDiffHaplosWithinParent)
export(subsetPedigree)
export(subsetVcfOnAllelicity)
export(summarizeLd)
export(summarizeLdPerChr)
export(summaryFasta)
export(summaryMcmcChain)
export(summaryVariant)
export(tableVcfAlt)
export(thinSnps)
export(tridiag)
export(updateJoinMap)
export(varqual2summary)
export(vcf2dosage)
export(vcf2genoClasses)
export(writeCartagene)
export(writeGenMapJoinMap)
export(writeGenosFimpute)
export(writeGenosFindhap)
export(writeInputsFastphase)
export(writeInputsFimpute)
export(writeInputsFindhap)
export(writePedFileFimpute)
export(writePedFileFindhap)
export(writePhenoJoinMap)
export(writeSegregJoinMap)
export(writeSnpInfoFimpute)
export(writeSnpInfoFindhap)
import(Matrix)
import(Rcpp)
import(data.table)
import(lme4)
import(stats)
importFrom(grDevices,rgb)
importFrom(graphics,arrows)
importFrom(graphics,axis)
importFrom(graphics,lines)
importFrom(graphics,par)
importFrom(graphics,segments)
importFrom(methods,is)