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/bioinfo_sequences.R R/breeding_game.R R/breeding_game_server.R R/breeding_game_ui.R R/fastPHASE.R R/geomaps.R R/grapevine.R R/misc.R R/molbio_plates.R R/plotting.R R/quantgen.R R/stats.R README.md
agpl-3.0.txt
gpl-3.0.txt
inst/CITATION
inst/breeding-game/server.R inst/breeding-game/ui.R
inst/extdata/example.vcf
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/chiSqSnpGenos.Rd man/chromNames2integers.Rd man/closeCarthagene.Rd man/coancestry2relmat.Rd man/confidenceGenoOneVar.Rd man/controlBayesFdr.Rd man/convertFactorColumnsToCharacter.Rd man/convertImputedTo012.Rd man/cor2cov.Rd man/corrMatAR1.Rd man/correspondenceJoinMap2qtl.Rd man/countGenotypicClasses.Rd man/countRequestedBreedTypes.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/dimVcf.Rd man/discardMarkersMissGenos.Rd man/discardSnpsLowMaf.Rd man/distConsecutiveSnps.Rd man/distSnpPairs.Rd man/doesBreederExist.Rd man/drawLocCrossovers.Rd man/emptyWells.Rd man/emreml.Rd man/estMrkOrderGenDistsWithCarthagene.Rd man/estimGenRel.Rd man/estimLd.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/formatReadCountsPerLane.Rd man/freadBedtoolsCoverageHist.Rd man/gcContent.Rd man/gemma.Rd man/gemmaUlmmPerChr.Rd man/genoClasses2JoinMap.Rd man/genoClasses2genoDoses.Rd man/genoDoses2ASMap.Rd man/genoDoses2Vcf.Rd man/genoDoses2bimbam.Rd man/genoDoses2genoClasses.Rd man/getBreedingGameSetup.Rd man/getHaplosInd.Rd man/getHaplosInds.Rd man/getIndNamesFromHaplos.Rd man/getMeanVarBetaDist.Rd man/getNbPCsMinimAvgSqPartCor.Rd man/getParamsBetaDist.Rd man/gibbsJanss2012.Rd man/gps2kml.Rd man/grSummaryPerBin.Rd man/gtVcf2dose.Rd man/gtVcf2genoClasses.Rd man/haplosAlleles2num.Rd man/haplosList2Matrix.Rd man/hinton.Rd man/imageWithScale.Rd man/imputeGenosWithMean.Rd man/imputeGenosWithMeanPerPop.Rd man/infoGeneticMap.Rd man/infoVariantCalls.Rd man/initPlates.Rd man/inlaAM.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/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/mme.Rd man/mpInv.Rd man/msd.Rd man/mummer2granges.Rd man/openCarthagene.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/plotAligns.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/plotMapSxGDomaineChapitre.Rd man/plotMcmcChain.Rd man/plotPca.Rd man/plotPedigree.Rd man/plotPhyVsGenDistances.Rd man/plotPlate.Rd man/plotVcfPercNa.Rd man/plotWithScale.Rd man/precMatAR1.Rd man/prettyPrintSummary.Rd man/pruneSnpsLd.Rd man/pve2beta.Rd man/qqplotPval.Rd man/qtlrelPerChr.Rd man/quantNorm.Rd man/quass.Rd man/randPlate.Rd man/readBcftoolsCounts.Rd man/readBiomercator.Rd man/readCheckBreedDataFile.Rd man/readCheckBreedPlantFile.Rd man/readGenosFastphase.Rd man/readGenosFimpute.Rd man/readHaplosFastphase.Rd man/readOutputsFimpute.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/requireNamespaces.Rd man/rmatnorm.Rd man/rmse.Rd man/rngVcf2df.Rd man/runCarthagene.Rd man/runFastphase.Rd man/runFimpute.Rd man/segSites2allDoses.Rd man/segSites2snpCoords.Rd man/seqIdStartEnd2GRanges.Rd man/setGt2Na.Rd man/setJoinMapPhasesFromParentalLinkGroups.Rd man/setUpBreedingGame.Rd man/setupQtlCrossObject.Rd man/significantTests.Rd man/simulAnimalModel.Rd man/simulBslmm.Rd man/simulBvsr.Rd man/simulCoalescent.Rd man/simulGenosDose.Rd man/simulLogistic.Rd man/simulRefAltSnpAlleles.Rd man/simulRefseqCompatibleWithVcf.Rd man/simulSnpEffectsTraits12.Rd man/simulTrait3.Rd man/simulTraits12.Rd man/splitGenomesTrainTest.Rd man/stanAM.Rd man/stanAMwriteModel.Rd man/statsAllPairAligns.Rd man/stopIfNotValidGenosDose.Rd man/stopIfNotValidHaplos.Rd man/subsetDiffHaplosWithinParent.Rd man/subsetVcfOnAllelicity.Rd man/summaryFasta.Rd man/summaryMcmcChain.Rd man/summaryVariant.Rd man/tableVcfAlt.Rd man/thinSnps.Rd man/updateJoinMap.Rd man/varqual2summary.Rd man/vcf2dosage.Rd man/vcf2genoClasses.Rd man/writeCartagene.Rd man/writeGenMapJoinMap.Rd man/writeGenosFimpute.Rd man/writeInputsFastphase.Rd man/writeInputsFimpute.Rd man/writePedFileFimpute.Rd man/writePhenoJoinMap.Rd man/writeSegregJoinMap.Rd man/writeSnpInfoFimpute.Rd misc/estim-heritability.Rmd misc/genetic-map_outbreds.Rmd misc/genotype-imputation.Rmd misc/intro-AR1.Rmd misc/intro-EM-algo.Rmd misc/intro-Gibbs-sampler.Rmd misc/intro-heteroscedasticity.Rmd misc/intro-mvAM.Rmd misc/quantgen-varsel.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
timflutre/rutilstimflutre documentation built on Dec. 14, 2017, 9:54 p.m.