Files in timflutre/rutilstimflutre
Timothee Flutre's personal R code
.Rbuildignore
.gitignore
COPYING
DESCRIPTION
NAMESPACE
R/CarthaGene.R
R/FImpute.R
R/GEMMA.R
R/apple.R
R/bioinfo_sequences.R
R/breeding_game.R
R/caret.R
R/fastPHASE.R
R/findhap.R
R/geomaps.R
R/grapevine.R
R/growth.R
R/misc.R
R/molbio_plates.R
R/plotting.R
R/popgen.R
R/qtl.R
R/quantgen.R
R/spatial.R
R/stats.R
README.md
agpl-3.0.txt
gpl-3.0.txt
inst/CITATION
inst/extdata/example.vcf
man/BBI.Rd
man/MIMQTL.Rd
man/SIMQTL.Rd
man/adjustPvaluesSidak.Rd
man/adjustThreshBonf.Rd
man/adjustThreshGalwey.Rd
man/adjustThreshSidak.Rd
man/aireml.Rd
man/allPairAligns.Rd
man/barplotGeneticMap.Rd
man/barplotInsertSizes.Rd
man/barplotReadCounts.Rd
man/betterSummary.Rd
man/binaryClassif.Rd
man/blast2granges.Rd
man/boxplotCandidateQtl.Rd
man/calcAsymptoticBayesFactorWakefield.Rd
man/calcAvgPwDiffBtwHaplos.Rd
man/calcExactBayesFactorServinStephens.Rd
man/calcFreqMissSnpGenosPerGeno.Rd
man/calcFreqMissSnpGenosPerSnp.Rd
man/calcFreqNaVcf.Rd
man/calcL10ApproximateBayesFactorWen.Rd
man/calcL10ApproximateBayesFactorWenStephens.Rd
man/caretFitBglr.Rd
man/caretFitQtl.Rd
man/caretFitRrblup.Rd
man/caretFitVarbvs.Rd
man/caretGridBglr.Rd
man/caretGridQtl.Rd
man/caretGridRrblup.Rd
man/caretGridVarbvs.Rd
man/caretPredictBglr.Rd
man/caretPredictQtl.Rd
man/caretPredictRrblup.Rd
man/caretPredictVarbvs.Rd
man/caretSummary.Rd
man/chiSqSnpGenos.Rd
man/chromNames2integers.Rd
man/closeCarthagene.Rd
man/clusteredness.Rd
man/coancestry2relmat.Rd
man/confidenceGenoOneVar.Rd
man/controlBayesFdr.Rd
man/convertFactorColumnsToCharacter.Rd
man/convertImputedTo012.Rd
man/convertVcfToGenoDoseWithBcftools.Rd
man/cor2cov.Rd
man/corrMatAR1.Rd
man/correctSpatialHeterogeneity.Rd
man/correspondenceJoinMap2qtl.Rd
man/countGenotypicClasses.Rd
man/covMatAR1.Rd
man/coverageBams.Rd
man/coverageRegions.Rd
man/createA.Rd
man/defLinkgroupsWithCarthagene.Rd
man/depthsPerRegion.Rd
man/depthsPerSample.Rd
man/descPlate.Rd
man/df2gr.Rd
man/dimVcf.Rd
man/discardMarkersMissGenos.Rd
man/discardSnpsLowMaf.Rd
man/distConsecutiveSnps.Rd
man/distSnpPairs.Rd
man/drawLocCrossovers.Rd
man/dsVcf2dose.Rd
man/effNbIndepTests.Rd
man/effNbIndepTestsPerChr.Rd
man/em_solve.Rd
man/emptyWells.Rd
man/emreml.Rd
man/estMrkOrderGenDistsWithCarthagene.Rd
man/estimGenRel.Rd
man/estimH2means.Rd
man/estimLd.Rd
man/estimLdPerChr.Rd
man/estimSnpAf.Rd
man/estimSnpMaf.Rd
man/estimatePi0WithEbf.Rd
man/estimatePi0WithQbf.Rd
man/extractFasta.Rd
man/fecundation.Rd
man/filterSegreg.Rd
man/filterVariantCalls.Rd
man/fitPhyDistVsLd.Rd
man/formatReadCountsPerLane.Rd
man/freadBedtoolsCoverageHist.Rd
man/gcContent.Rd
man/gemma.Rd
man/gemmaUlmmPerChr.Rd
man/genoAr1Coef.Rd
man/genoClasses2JoinMap.Rd
man/genoClasses2genoDoses.Rd
man/genoDoses2ASMap.Rd
man/genoDoses2Vcf.Rd
man/genoDoses2bimbam.Rd
man/genoDoses2genoClasses.Rd
man/getBreedingGameConstants.Rd
man/getBreedingGameSetup.Rd
man/getHaplosInd.Rd
man/getHaplosInds.Rd
man/getIndNamesFromHaplos.Rd
man/getJoinMapSegregs.Rd
man/getMeanVarBetaDist.Rd
man/getNbPCsMinimAvgSqPartCor.Rd
man/getParamsBetaDist.Rd
man/getSamplesFromVcfFile.Rd
man/getSsrGenosFromPlantGrapePdf.Rd
man/gibbsJanss2012.Rd
man/gps2kml.Rd
man/grSummaryPerBin.Rd
man/gtVcf2dose.Rd
man/gtVcf2genoClasses.Rd
man/h2v1WX2019.Rd
man/h2v2WX2019.Rd
man/haplosAlleles2num.Rd
man/haplosList2Matrix.Rd
man/hinton.Rd
man/imageWithScale.Rd
man/imputeGenosWithMean.Rd
man/imputeGenosWithMeanPerPop.Rd
man/indexGenoDoses.Rd
man/indexVcfFile.Rd
man/infoGeneticMap.Rd
man/infoVariantCalls.Rd
man/initPlates.Rd
man/inlaAM.Rd
man/inlineFctForm.Rd
man/invertGRanges.Rd
man/isSingular.Rd
man/jagsAM.Rd
man/joinMap2backcross.Rd
man/joinMap2designMatrix.Rd
man/lengthenPlate.Rd
man/lmerAM.Rd
man/loadBlast.Rd
man/loadMummer.Rd
man/loadPlates.Rd
man/loadReadCountsPerIndAndLane.Rd
man/lodLinkage.Rd
man/log10WeightedSum.Rd
man/mae.Rd
man/maf2genoFreq.Rd
man/make.formula.Rd
man/makeCross.Rd
man/makeCrosses.Rd
man/makeDfInitPhenos.Rd
man/makeDfPhenos.Rd
man/makeExampleDataFile.Rd
man/makeExamplePlantFile.Rd
man/makeGameteSingleInd.Rd
man/makeGameteSingleIndSingleChrom.Rd
man/makeGridWenStephens.Rd
man/makeMmeElements.Rd
man/makeMmeLhs.Rd
man/makeMmeRhs.Rd
man/matWide2Long.Rd
man/matrixTrace.Rd
man/mergeOverlaps.Rd
man/mpInv.Rd
man/msd.Rd
man/mummer2granges.Rd
man/n0WX2019.Rd
man/openCarthagene.Rd
man/orthoRotate2D.Rd
man/parseCgGroup.Rd
man/parseCgHeaprint.Rd
man/parseCgMaprintd.Rd
man/parseCgMrkinfo.Rd
man/parseCgPwMatrix.Rd
man/pca.Rd
man/permuteAllelesInGenosDose.Rd
man/permuteAllelesInHaplosNum.Rd
man/phasedJoinMapCP2qtl.Rd
man/plantTrialLmmFitCompSel.Rd
man/plotAligns.Rd
man/plotFalconer.Rd
man/plotGRanges.Rd
man/plotGridMissGenos.Rd
man/plotHaplosMatrix.Rd
man/plotHistAllelFreq.Rd
man/plotHistMinAllelFreq.Rd
man/plotHistPval.Rd
man/plotInfoVariantCalls.Rd
man/plotLd.Rd
man/plotLdSry.Rd
man/plotMapSxGDomaineChapitre.Rd
man/plotMcmcChain.Rd
man/plotPca.Rd
man/plotPedigree.Rd
man/plotPhyDistVsLdSry.Rd
man/plotPhyVsGenDistances.Rd
man/plotPlate.Rd
man/plotResidualsBtwYears.Rd
man/plotVcfPercNa.Rd
man/plotWithScale.Rd
man/powerWX2019.Rd
man/precMatAR1.Rd
man/prettyPrintBetterSummary.Rd
man/pruneSnpsLd.Rd
man/pseudoR2.Rd
man/pve2beta.Rd
man/qqplotPval.Rd
man/qtlrelPerChr.Rd
man/quantNorm.Rd
man/quantilesBinnedSnpData.Rd
man/quass.Rd
man/randPlate.Rd
man/readBcftoolsCounts.Rd
man/readBiomercator.Rd
man/readGenoDoseFileFromBcftools.Rd
man/readGenosFastphase.Rd
man/readGenosFimpute.Rd
man/readGenosFindhap.Rd
man/readHaplosFastphase.Rd
man/readOutSTRUCTURE.Rd
man/readOutputsFimpute.Rd
man/readOutputsFindhap.Rd
man/readPlinkMendel.Rd
man/readSamDict.Rd
man/readSegregJoinMap.Rd
man/readVcfSubset.Rd
man/rearrangeInputsForAssoGenet.Rd
man/recodeGenosMinorSnpAllele.Rd
man/recodeIntoDominant.Rd
man/reformatGenoClasses.Rd
man/regplot.Rd
man/removeFileExtension.Rd
man/renameVcfSamples.Rd
man/requireNamespaces.Rd
man/rhoWX2019.Rd
man/rmatnorm.Rd
man/rmse.Rd
man/rngVcf2df.Rd
man/runCarthagene.Rd
man/runFastphase.Rd
man/runFimpute.Rd
man/runFindhap.Rd
man/sampleWX2019.Rd
man/segSites2allDoses.Rd
man/segSites2snpCoords.Rd
man/seqIdStartEnd2GRanges.Rd
man/setGt2Na.Rd
man/setJoinMapPhasesFromParentalLinkGroups.Rd
man/setupQtlCrossObject.Rd
man/significantTests.Rd
man/simulAnimalModel.Rd
man/simulAr1Ar1.Rd
man/simulBslmm.Rd
man/simulBvsr.Rd
man/simulCoalescent.Rd
man/simulGeneralisedLogistic.Rd
man/simulGenosDose.Rd
man/simulLogistic.Rd
man/simulRefAltSnpAlleles.Rd
man/simulRefseqCompatibleWithVcf.Rd
man/simulSnpEffectsTraits12.Rd
man/simulTrait3.Rd
man/simulTraits12.Rd
man/snpCoordsDf2Gr.Rd
man/solveMme.Rd
man/sortVcfFile.Rd
man/splitGenomesTrainTest.Rd
man/stanAM.Rd
man/stanAMwriteModel.Rd
man/statsAllPairAligns.Rd
man/statsStrongAssign.Rd
man/stopIfNotValidGenosDose.Rd
man/stopIfNotValidHaplos.Rd
man/structure2clumpp.Rd
man/subsetDiffHaplosWithinParent.Rd
man/subsetPedigree.Rd
man/subsetVcfOnAllelicity.Rd
man/summarizeLd.Rd
man/summarizeLdPerChr.Rd
man/summaryFasta.Rd
man/summaryMcmcChain.Rd
man/summaryVariant.Rd
man/tableVcfAlt.Rd
man/thinSnps.Rd
man/tridiag.Rd
man/updateJoinMap.Rd
man/varqual2summary.Rd
man/vcf2dosage.Rd
man/vcf2genoClasses.Rd
man/writeCartagene.Rd
man/writeGenMapJoinMap.Rd
man/writeGenosFimpute.Rd
man/writeGenosFindhap.Rd
man/writeInputsFastphase.Rd
man/writeInputsFimpute.Rd
man/writeInputsFindhap.Rd
man/writePedFileFimpute.Rd
man/writePedFileFindhap.Rd
man/writePhenoJoinMap.Rd
man/writeSegregJoinMap.Rd
man/writeSnpInfoFimpute.Rd
man/writeSnpInfoFindhap.Rd
misc/alternate-bearing.Rmd
misc/corr-spat-het.Rmd
misc/estim-heritability.Rmd
misc/gblup-pop-struct.Rmd
misc/genetic-map_outbreds.Rmd
misc/genotype-imputation_family_fimpute.Rmd
misc/genotype-imputation_population_beagle.Rmd
misc/genotype-imputation_population_fastphase.Rmd
misc/gwas-power-analysis.Rmd
misc/intro-AR1.Rmd
misc/intro-EM-algo.Rmd
misc/intro-Gibbs-sampler.Rmd
misc/intro-MMEs.Rmd
misc/intro-Price-eq.Rmd
misc/intro-breeder-eq.Rmd
misc/intro-het-GxE.Rmd
misc/intro-heteroscedasticity.Rmd
misc/intro-mvAM.Rmd
misc/microplot_surface.Rmd
misc/parentage-analysis.Rmd
misc/perennial-fruit-plant-biparental-design.Rmd
misc/quantgen-varsel.Rmd
misc/quantgen_NOIA.Rmd
misc/simul-pop-struct.Rmd
misc/test-TMB.Rmd
misc/tuto-parallel.Rmd
misc/tuto_contrasts.Rmd
misc/tuto_varpart.Rmd
misc/two-phase_quantgen-analysis.Rmd
misc/use-caret-own-model.Rmd
rutilstimflutre.Rproj
tests/testthat.R
tests/testthat/test_FImpute.R
tests/testthat/test_VarCompEstimReml.R
tests/testthat/test_bioinfo_sequences.R
tests/testthat/test_breeding_game.R
tests/testthat/test_misc.R
tests/testthat/test_molbio_plates.R
tests/testthat/test_quantgen.R
tests/testthat/test_stats.R
vignettes/intro-bayes_univ-normal_unknown-mean-precision.Rmd
vignettes/priors-regression.Rmd
