API for timflutre/rutilstimflutre
Timothee Flutre's personal R code

Global functions
aireml Man page Source code
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 Source code
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 Source code
calcL10ApproximateBayesFactorWen Man page Source code
calcL10ApproximateBayesFactorWenStephens Man page Source code
chiSqSnpGenos Man page Source code
chromNames2integers Man page Source code
closeCarthagene Man page Source code
coancestry2relmat Man page Source code
confidenceGenoOneVar Man page Source code
controlBayesFdr Man page Source code
convertFactorColumnsToCharacter Man page Source code
convertImputedTo012 Man page Source code
cor2cov Man page Source code
corrMatAR1 Man page Source code
correspondenceJoinMap2qtl Man page Source code
countGenotypicClasses Man page Source code
countRequestedBreedTypes Man page Source code
covMatAR1 Man page Source code
coverageBams Man page Source code
coverageRegions Man page Source code
createA Man page Source code
defLinkgroupsWithCarthagene Man page Source code
depthsPerRegion Man page Source code
depthsPerSample Man page Source code
descPlate Man page Source code
df2gr Source code
dimVcf Man page Source code
discardMarkersMissGenos Man page Source code
discardSnpsLowMaf Man page Source code
distConsecutiveSnps Man page Source code
distSnpPairs Man page Source code
doesBreederExist Man page Source code
drawLocCrossovers Man page Source code
emptyWells Man page Source code
emreml Man page Source code
estMrkOrderGenDistsWithCarthagene Man page Source code
estimGenRel Man page Source code
estimLd 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 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
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
getBreedingGameSetup Man page Source code
getHaplosInd Man page Source code
getHaplosInds Man page Source code
getIndNamesFromHaplos Man page Source code
getMeanVarBetaDist Man page Source code
getNbPCsMinimAvgSqPartCor Man page Source code
getParamsBetaDist Man page Source code
getSegregatingLocusPerParent Source code
gibbsJanss2012 Man page Source code
gps2kml Man page Source code
grSummaryPerBin Man page Source code
gtVcf2dose Man page Source code
gtVcf2genoClasses Man page Source code
haplosAlleles2num Man page Source code
haplosList2Matrix Man page Source code
hinton Man page Source code
imageWithScale Man page Source code
imputeGenosWithMean Man page Source code
imputeGenosWithMeanPerPop Man page Source code
infoGeneticMap Man page Source code
infoVariantCalls Man page Source code
initPlates Man page Source code
inlaAM Man page Source code
invertGRanges Man page Source code
isSingular Man page Source code
jagsAM 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 Source code
loadMummer Man page Source code
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
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
mme Man page Source code
mpInv Man page Source code
msd Man page Source code
mummer2granges Man page Source code
onAttach Source code
openCarthagene 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
plotAligns Man page Source code
plotGRanges Man page Source code
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 Source code
plotLd Man page Source code
plotMapSxGDomaineChapitre Man page Source code
plotMcmcChain Man page Source code
plotPca Man page Source code
plotPedigree Man page Source code
plotPhyVsGenDistances Man page Source code
plotPlate Man page Source code
plotVcfPercNa Man page Source code
plotWithScale Man page Source code
precMatAR1 Man page Source code
prettyPrintSummary Man page Source code
pruneSnpsLd Man page Source code
pve2beta Man page Source code
qqplotPval Man page Source code
qtlrelPerChr Man page Source code
quantNorm Man page Source code
quass Man page Source code
randPlate Man page Source code
readBcftoolsCounts Man page Source code
readBiomercator Man page Source code
readCheckBreedDataFile Man page Source code
readCheckBreedPlantFile Man page Source code
readGenosFastphase Man page Source code
readGenosFimpute Man page Source code
readHaplosFastphase Man page Source code
readOutputsFimpute Man page Source code
readPlinkMendel Man page Source code
readSamDict Man page Source code
readSegregJoinMap Man page Source code
readVcfSubset Man page Source code
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
requireNamespaces Man page Source code
rmatnorm Man page Source code
rmse Man page Source code
rngVcf2df Man page Source code
runCarthagene Man page Source code
runFastphase Man page Source code
runFimpute Man page Source code
sValidSnpCoords Source code
segSites2allDoses Man page Source code
segSites2snpCoords Man page Source code
seqIdStartEnd2GRanges Man page Source code
setGt2Na Man page Source code
setJoinMapPhasesFromParentalLinkGroups Man page Source code
setUpBreedingGame Man page Source code
setupQtlCrossObject Man page Source code
significantTests Man page Source code
simulAnimalModel Man page Source code
simulBslmm Man page Source code
simulBvsr Man page Source code
simulCoalescent Man page Source code
simulGenosDose Man page Source code
simulLogistic Man page Source code
simulRefAltSnpAlleles Man page Source code
simulRefseqCompatibleWithVcf Man page Source code
simulSnpEffectsTraits12 Man page Source code
simulTrait3 Man page Source code
simulTraits12 Man page Source code
splitGenomesTrainTest Man page Source code
stanAM Man page Source code
stanAMwriteModel Man page Source code
statsAllPairAligns Man page Source code
stopIfNotValidGenosDose Man page Source code
stopIfNotValidHaplos Man page Source code
subsetDiffHaplosWithinParent Man page Source code
subsetVcfOnAllelicity Man page Source code
summaryFasta Man page Source code
summaryMcmcChain Man page Source code
summaryVariant Man page Source code
tableVcfAlt Man page Source code
thinSnps Man page Source code
updateJoinMap Man page Source code
varqual2summary Man page Source code
vcf2dosage Man page Source code
vcf2genoClasses Man page Source code
writeCartagene Man page Source code
writeGenMapJoinMap Man page Source code
writeGenosFimpute Man page Source code
writeInputsFastphase Man page Source code
writeInputsFimpute Man page Source code
writePedFileFimpute Man page Source code
writePhenoJoinMap Man page Source code
writeSegregJoinMap Man page Source code
writeSnpInfoFimpute Man page Source code
timflutre/rutilstimflutre documentation built on Dec. 14, 2017, 9:54 p.m.