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