Man pages for timflutre/rutilstimflutre
Timothee Flutre's personal R code

airemlEstimate variance components via REML using AI
allPairAlignsAll pairwise alignments
barplotGeneticMapStacked barplot of markers
barplotInsertSizesBar plot of insert sizes
barplotReadCountsStacked barplot of read counts
betterSummaryBetter summary
binaryClassifHypothesis testing
blast2grangesBLAST
boxplotCandidateQtlBoxplot of QTL
calcAsymptoticBayesFactorWakefieldAsymptotic Bayes factor
calcAvgPwDiffBtwHaplosPi
calcExactBayesFactorServinStephensExact Bayes factor
calcFreqMissSnpGenosPerGenoMissing genotypes
calcFreqMissSnpGenosPerSnpMissing genotypes
calcFreqNaVcfMissing genotypes in VCF
calcL10ApproximateBayesFactorWenApproximate Bayes factor
calcL10ApproximateBayesFactorWenStephensApproximate Bayes factor
chiSqSnpGenosChi-squared for Hardy-Weinberg
chromNames2integersRename chromosomes
closeCarthageneClose CarthaGene
coancestry2relmatGenetic relatedness
confidenceGenoOneVarConfidence in one variant's genotypes
controlBayesFdrFDR
convertFactorColumnsToCharacterData.frame
convertImputedTo012Convert imputed genotypes to 0/1/2
convertVcfToGenoDoseWithBcftoolsConvert VCF file to dosage file
cor2covScales a correlation matrix into the corresponding covariance...
correspondenceJoinMap2qtlJoinMap/MapQTL to R/qtl
corrMatAR1AR(1)
countGenotypicClassesGenotypic classes
coverageBamsCoverage
coverageRegionsPlot the covered fraction of regions as a function of depth
covMatAR1AR(1)
createACompute the inverse of the additive relationship matrix using...
defLinkgroupsWithCarthageneDefine linkage groups with CarthaGene
depthsPerRegionDepth per region across samples
depthsPerSampleDepth per sample across regions
descPlateDescribe plate
dimVcfVCF dimensions
discardMarkersMissGenosMissing genotypes
discardSnpsLowMafMinor allele frequencies
distConsecutiveSnpsDistance between consecutive SNPs
distSnpPairsDistance between SNP pairs
drawLocCrossoversCrossing-overs
dsVcf2doseConvert DS to dosage
emptyWellsFind empty wells
emremlEstimate variance components via REML using EM
em_solveEM algorithm
estimatePi0WithEbfFDR
estimatePi0WithQbfFDR
estimGenRelGenomic relatedness
estimLdPairwise linkage disequilibrium
estimSnpAfAllele frequencies
estimSnpMafMinor allele frequencies
estMrkOrderGenDistsWithCarthageneEstimate marker order and genetic distances with CarthaGene
extractFastaFasta file
fecundationFecundation
filterSegregFilter for segregation
filterVariantCallsFilter variant calls
formatReadCountsPerLaneReformat read counts per lane
freadBedtoolsCoverageHistRead bedtools-coverage-hist as data.table
gcContentCalculate the GC content of a set of sequences
gemmaGEMMA
gemmaUlmmPerChrGEMMA uLMM per chromosome
genoClasses2genoDosesConvert genotypes
genoClasses2JoinMapConvert genotypes
genoDoses2ASMapConvert genotypes
genoDoses2bimbamConvert genotypes
genoDoses2genoClassesConvert genotypes
genoDoses2VcfConvert genotypes
getBreedingGameConstantsGet the breeding game constants
getBreedingGameSetupGet the breeding game setup
getHaplosIndHaplotypes of an genotype
getHaplosIndsHaplotypes of several genotypes
getIndNamesFromHaplosGenotype names
getMeanVarBetaDistBeta distribution
getNbPCsMinimAvgSqPartCorChoose the number of PCs
getParamsBetaDistBeta distribution
getSamplesFromVcfFileSamples from VCF file
gibbsJanss2012Gibbs sampler from Janss et al (2012)
gps2kmlConvert GPS coordinates
grSummaryPerBinGenomic bins
gtVcf2doseConvert GT to dosage
gtVcf2genoClassesParse VCF
haplosAlleles2numHaplotypes
haplosList2MatrixConvert haplotypes
hintonHinton diagram
imageWithScalePlot a matrix as a heatmap in its natural orientation, with a...
imputeGenosWithMeanGenotype imputation
imputeGenosWithMeanPerPopGenotype imputation
indexVcfFileIndex a VCF file
infoGeneticMapInfo about a given genetic map
infoVariantCallsInformation on variant-level calls
initPlatesInitialize plate(s)
inlaAMAnimal model
invertGRangesInvert GRanges
isSingularSingular matrix
jagsAMAnimal model
joinMap2backcrossGenotype coding
joinMap2designMatrixGenotype coding
lengthenPlateLengthen plate
lmerAMAnimal model
loadBlastBLAST
loadMummerMUMmer
loadPlatesLoad plate(s)
loadReadCountsPerIndAndLaneLoad read counts
lodLinkageTest for linkage
log10WeightedSumLog of weighted sum
maeMean absolute error
maf2genoFreqGenotype frequencies
makeCrossCross
makeCrossesCrosses
makeDfInitPhenosSimul breeding game
makeDfPhenosSimul breeding game
makeExampleDataFileExample for breeding game
makeExamplePlantFileExample for breeding game
makeGameteSingleIndGamete
makeGameteSingleIndSingleChromGamete
makeGridWenStephensGrid for Bayes Factors
makeMmeElementsMake elements of MME
makeMmeLhsMake MME's left-hand side
makeMmeRhsMake MME's right-hand side
mpInvMoore-Penrose pseudo-inverse
msdMean signed difference
mummer2grangesMUMmer
openCarthageneOpen CarthaGene
parseCgGroupParse CarthaGene's output
parseCgHeaprintParse CarthaGene's output
parseCgMaprintdParse CarthaGene's output
parseCgMrkinfoParse CarthaGene's output
parseCgPwMatrixParse CarthaGene's output
pcaPrincipal component analysis
permuteAllelesInGenosDoseGenotypes
permuteAllelesInHaplosNumHaplotypes
phasedJoinMapCP2qtlGenotype coding
plotAlignsPlot alignments
plotGRangesPlot GRanges
plotGridMissGenosMissing genotypes
plotHaplosMatrixHaplotypes
plotHistAllelFreqAllele frequencies
plotHistMinAllelFreqMinor allele frequencies
plotHistPvalP values
plotInfoVariantCallsPlot information on variant-level calls
plotLdPairwise linkage disequilibrium
plotMapSxGDomaineChapitrePlot the map of SxG
plotMcmcChainMCMC diagnostics
plotPcaPrincipal component analysis
plotPedigreePlot pedigree
plotPhyVsGenDistancesPlot physical versus genetic distances
plotPlatePlot plate
plotVcfPercNaPlot VCF
plotWithScalePlot a scale, e.g. to add on the side of image()
precMatAR1AR(1)
prettyPrintBetterSummaryPrint better summary
pruneSnpsLdPrune SNPs based on LD
pve2betaProportion of variance explained
qqplotPvalQ-Q plot for p values
qtlrelPerChrQTLRel per chromosome
quantilesBinnedSnpDataQuantiles of allelic R2 after binning
quantNormQuantile-normalize a vector of numbers to a standard normal...
quassCompute the inverse of the additive relationship matrix using...
randPlateRandomize plate
readBcftoolsCountsRead output from bcftools counts
readBiomercatorReturns the genetic map contained in a BioMercator TXT file.
readGenoDoseFileFromBcftoolsRead SNP genotypes as dosage from bcftools
readGenosFastphaseRead genotypes from fastPHASE
readGenosFimputeRead genotypes from FImpute
readGenosFindhapRead genotypes from findhap
readHaplosFastphaseRead haplotypes from fastPHASE
readOutputsFimputeRead outputs from FImpute
readOutputsFindhapRead outputs from findhap
readPlinkMendelRead PLINK
readSamDictRead SAM dict
readSegregJoinMapRead genotypes for JoinMap/MapQTL
readVcfSubsetRead VCF
rearrangeInputsForAssoGenetPlant association genetics
recodeGenosMinorSnpAlleleMinor allele frequencies
recodeIntoDominantSNP genotypes
reformatGenoClassesConvert genotypes
regplotScatter plot with regression lines
removeFileExtensionFile
renameVcfSamplesRename VCF samples
requireNamespacesNamespaces
rmatnormMatrix-variate Normal distribution
rmseRoot mean squared error
rngVcf2dfConvert ranges to data.frame
runCarthageneRun a CarthaGene command
runFastphaseGenotype imputation via fastPHASE
runFimputeGenotype imputation via FImpute
runFindhapGenotype imputation via findhap
segSites2allDosesSite frequency spectrum
segSites2snpCoordsSite frequency spectrum
seqIdStartEnd2GRangesMake GRanges
setGt2NaSet GT to NA
setJoinMapPhasesFromParentalLinkGroupsGenotype coding
setUpBreedingGameSet up breeding game
setupQtlCrossObjectSet-up a R/qtl "cross" object
significantTestsMultiple tests correction
simulAnimalModelAnimal model
simulBslmmBSLMM
simulBvsrBVSR
simulCoalescentCoalescent with recombination
simulGeneralisedLogisticGeneralised logistic growth (Richards' curve)
simulGenosDoseGenotypes
simulLogisticLogistic growth
simulRefAltSnpAllelesSNP alleles
simulRefseqCompatibleWithVcfFasta file
simulSnpEffectsTraits12Simul breeding game
simulTrait3Simul breeding game
simulTraits12Simul breeding game
snpCoordsDf2GrSNP coordinates from data frame to GRanges
solveMmeSolve MME
sortVcfFileSort a VCF file
splitGenomesTrainTestGenomes
stanAMAnimal model
stanAMwriteModelAnimal model
statsAllPairAlignsExtract statistics from all pairwise alignments
stopIfNotValidGenosDoseGenotypes
stopIfNotValidHaplosHaplotypes
subsetDiffHaplosWithinParentHaplotypes
subsetPedigreeSubset a pedigree
subsetVcfOnAllelicityParse VCF
summaryFastaFasta file
summaryMcmcChainMCMC results
summaryVariantSummary per variant
tableVcfAltRead VCF
thinSnpsThin SNPs
updateJoinMapJoinMap format
varqual2summarySummary per variant
vcf2dosageConvert VCF to dose
vcf2genoClassesConvert VCF to genotypic classes
writeCartageneGenotype coding
writeGenMapJoinMapWrite genetic map for JoinMap/MapQTL
writeGenosFimputeWrite SNP genotypes for FImpute
writeGenosFindhapWrite SNP genotypes for findhap
writeInputsFastphaseWrite inputs for fastPHASE
writeInputsFimputeWrite inputs for FImpute
writeInputsFindhapWrite inputs for findhap
writePedFileFimputeWrite pedigree for FImpute
writePedFileFindhapWrite pedigree for findhap
writePhenoJoinMapWrite phenotypes for JoinMap/MapQTL
writeSegregJoinMapWrite genotypes for JoinMap/MapQTL
writeSnpInfoFimputeWrite SNP information for FImpute
writeSnpInfoFindhapWrite SNP information for findhap
timflutre/rutilstimflutre documentation built on July 5, 2018, 10:41 p.m.