Man pages for timflutre/rutilstimflutre
Timothee Flutre's personal R code
| adjustPvaluesSidak | Multiple testing |
| adjustThreshBonf | Multiple testing |
| adjustThreshGalwey | Multiple testing |
| adjustThreshSidak | Multiple testing |
| aireml | Estimate variance components via REML using AI |
| allPairAligns | All pairwise alignments |
| barplotGeneticMap | Stacked barplot of markers |
| barplotInsertSizes | Bar plot of insert sizes |
| barplotReadCounts | Stacked barplot of read counts |
| BBI | Biennial bearing index |
| betterSummary | Better summary |
| binaryClassif | Hypothesis testing |
| blast2granges | BLAST |
| boxplotCandidateQtl | Boxplot of QTL |
| calcAsymptoticBayesFactorWakefield | Asymptotic Bayes factor |
| calcAvgPwDiffBtwHaplos | Pi |
| calcExactBayesFactorServinStephens | Exact Bayes factor |
| calcFreqMissSnpGenosPerGeno | Missing genotypes |
| calcFreqMissSnpGenosPerSnp | Missing genotypes |
| calcFreqNaVcf | Missing genotypes in VCF |
| calcL10ApproximateBayesFactorWen | Approximate Bayes factor |
| calcL10ApproximateBayesFactorWenStephens | Approximate Bayes factor |
| caretFitBglr | Fit with BGLR for caret |
| caretFitQtl | Fit with qtl for caret |
| caretFitRrblup | Fit with rrBLUP for caret |
| caretFitVarbvs | Fit with varbvs for caret |
| caretGridBglr | Grid with BGLR for caret |
| caretGridQtl | Grid with qtl for caret |
| caretGridRrblup | Grid with rrBLUP for caret |
| caretGridVarbvs | Grid with varbvs for caret |
| caretPredictBglr | Predict with BGLR for caret |
| caretPredictQtl | Predict with qtl for caret |
| caretPredictRrblup | Predict with rrBLUP for caret |
| caretPredictVarbvs | Predict with varbvs for caret |
| caretSummary | Summary for caret |
| chiSqSnpGenos | Chi-squared for Hardy-Weinberg |
| chromNames2integers | Rename chromosomes |
| closeCarthagene | Close CarthaGene |
| clusteredness | Clusteredness |
| coancestry2relmat | Genetic relatedness |
| confidenceGenoOneVar | Confidence in one variant's genotypes |
| controlBayesFdr | FDR |
| convertFactorColumnsToCharacter | Data.frame |
| convertImputedTo012 | Convert imputed genotypes to 0/1/2 |
| convertVcfToGenoDoseWithBcftools | Convert VCF file to dosage file |
| cor2cov | Scales a correlation matrix into the corresponding covariance... |
| correctSpatialHeterogeneity | Correct spatial heterogeneity |
| correspondenceJoinMap2qtl | JoinMap/MapQTL to R/qtl |
| corrMatAR1 | AR(1) |
| countGenotypicClasses | Genotypic classes |
| coverageBams | Coverage |
| coverageRegions | Plot the covered fraction of regions as a function of depth |
| covMatAR1 | AR(1) |
| createA | Compute the inverse of the additive relationship matrix using... |
| defLinkgroupsWithCarthagene | Define linkage groups with CarthaGene |
| depthsPerRegion | Depth per region across samples |
| depthsPerSample | Depth per sample across regions |
| descPlate | Describe plate |
| df2gr | Convert data frame to GRanges |
| dimVcf | VCF dimensions |
| discardMarkersMissGenos | Missing genotypes |
| discardSnpsLowMaf | Minor allele frequencies |
| distConsecutiveSnps | Distance between consecutive SNPs |
| distSnpPairs | Distance between SNP pairs |
| drawLocCrossovers | Crossing-overs |
| dsVcf2dose | Convert DS to dosage |
| effNbIndepTests | Multiple testing |
| effNbIndepTestsPerChr | Multiple testing |
| emptyWells | Find empty wells |
| emreml | Estimate variance components via REML using EM |
| em_solve | EM algorithm |
| estimatePi0WithEbf | FDR |
| estimatePi0WithQbf | FDR |
| estimGenRel | Genomic relatedness |
| estimH2means | Broad-sense heritability |
| estimLd | Pairwise linkage disequilibrium |
| estimLdPerChr | Pairwise linkage disequilibrium |
| estimSnpAf | Allele frequencies |
| estimSnpMaf | Minor allele frequencies |
| estMrkOrderGenDistsWithCarthagene | Estimate marker order and genetic distances with CarthaGene |
| extractFasta | Fasta file |
| fecundation | Fecundation |
| filterSegreg | Filter for segregation |
| filterVariantCalls | Filter variant calls |
| fitPhyDistVsLd | Pairwise linkage disequilibrium |
| formatReadCountsPerLane | Reformat read counts per lane |
| freadBedtoolsCoverageHist | Read bedtools-coverage-hist as data.table |
| gcContent | Calculate the GC content of a set of sequences |
| gemma | GEMMA |
| gemmaUlmmPerChr | GEMMA uLMM per chromosome |
| genoAr1Coef | Genotypic values for fruit bearing |
| genoClasses2genoDoses | Convert genotypes |
| genoClasses2JoinMap | Convert genotypes |
| genoDoses2ASMap | Convert genotypes |
| genoDoses2bimbam | Convert genotypes |
| genoDoses2genoClasses | Convert genotypes |
| genoDoses2Vcf | Convert genotypes |
| getBreedingGameConstants | Get the breeding game constants |
| getBreedingGameSetup | Get the breeding game setup |
| getHaplosInd | Haplotypes of an genotype |
| getHaplosInds | Haplotypes of several genotypes |
| getIndNamesFromHaplos | Genotype names |
| getJoinMapSegregs | JoinMap segregation types |
| getMeanVarBetaDist | Beta distribution |
| getNbPCsMinimAvgSqPartCor | Choose the number of PCs |
| getParamsBetaDist | Beta distribution |
| getSamplesFromVcfFile | Samples from VCF file |
| getSsrGenosFromPlantGrapePdf | SSR genotypes from PlantGrape |
| gibbsJanss2012 | Gibbs sampler from Janss et al (2012) |
| gps2kml | Convert GPS coordinates |
| grSummaryPerBin | Genomic bins |
| gtVcf2dose | Convert GT to dosage |
| gtVcf2genoClasses | Parse VCF |
| h2v1WX2019 | GWAS power analysis |
| h2v2WX2019 | GWAS power analysis |
| haplosAlleles2num | Haplotypes |
| haplosList2Matrix | Convert haplotypes |
| hinton | Hinton diagram |
| imageWithScale | Plot a matrix as a heatmap in its natural orientation, with a... |
| imputeGenosWithMean | Genotype imputation |
| imputeGenosWithMeanPerPop | Genotype imputation |
| indexGenoDoses | Index the dose of each SNP genotype |
| indexVcfFile | Index a VCF file |
| infoGeneticMap | Info about a given genetic map |
| infoVariantCalls | Information on variant-level calls |
| initPlates | Initialize plate(s) |
| inlaAM | Animal model |
| inlineFctForm | Inline function in formula |
| invertGRanges | Invert GRanges |
| isSingular | Singular matrix |
| jagsAM | Animal model |
| joinMap2backcross | Genotype coding |
| joinMap2designMatrix | Genotype coding |
| lengthenPlate | Lengthen plate |
| lmerAM | Animal model |
| loadBlast | BLAST |
| loadMummer | MUMmer |
| loadPlates | Load plate(s) |
| loadReadCountsPerIndAndLane | Load read counts |
| lodLinkage | Test for linkage |
| log10WeightedSum | Log of weighted sum |
| mae | Mean absolute error |
| maf2genoFreq | Genotype frequencies |
| makeCross | Cross |
| makeCrosses | Crosses |
| makeDfInitPhenos | Simul breeding game |
| makeDfPhenos | Simul breeding game |
| makeExampleDataFile | Example for breeding game |
| makeExamplePlantFile | Example for breeding game |
| make.formula | make.formula |
| makeGameteSingleInd | Gamete |
| makeGameteSingleIndSingleChrom | Gamete |
| makeGridWenStephens | Grid for Bayes Factors |
| makeMmeElements | Make elements of MME |
| makeMmeLhs | Make MME's left-hand side |
| makeMmeRhs | Make MME's right-hand side |
| matrixTrace | Trace of a matrix |
| matWide2Long | Reformat |
| mergeOverlaps | Merge overlapping genomic intervals |
| MIMQTL | QTL detection by MIM |
| mpInv | Moore-Penrose pseudo-inverse |
| msd | Mean signed difference |
| mummer2granges | MUMmer |
| n0WX2019 | GWAS power analysis |
| openCarthagene | Open CarthaGene |
| orthoRotate2D | Rotation |
| parseCgGroup | Parse CarthaGene's output |
| parseCgHeaprint | Parse CarthaGene's output |
| parseCgMaprintd | Parse CarthaGene's output |
| parseCgMrkinfo | Parse CarthaGene's output |
| parseCgPwMatrix | Parse CarthaGene's output |
| pca | Principal component analysis |
| permuteAllelesInGenosDose | Genotypes |
| permuteAllelesInHaplosNum | Haplotypes |
| phasedJoinMapCP2qtl | Genotype coding |
| plantTrialLmmFitCompSel | Model fit, comparison and selection |
| plotAligns | Plot alignments |
| plotFalconer | Falconer's parameterization |
| plotGRanges | Plot GRanges |
| plotGridMissGenos | Missing genotypes |
| plotHaplosMatrix | Haplotypes |
| plotHistAllelFreq | Allele frequencies |
| plotHistMinAllelFreq | Minor allele frequencies |
| plotHistPval | P values |
| plotInfoVariantCalls | Plot information on variant-level calls |
| plotLd | Pairwise linkage disequilibrium |
| plotLdSry | Pairwise linkage disequilibrium |
| plotMapSxGDomaineChapitre | Plot the map of SxG |
| plotMcmcChain | MCMC diagnostics |
| plotPca | Principal component analysis |
| plotPedigree | Plot pedigree |
| plotPhyDistVsLdSry | Pairwise linkage disequilibrium |
| plotPhyVsGenDistances | Plot physical versus genetic distances |
| plotPlate | Plot plate |
| plotResidualsBtwYears | Plot residuals between years |
| plotVcfPercNa | Plot VCF |
| plotWithScale | Plot a scale, e.g. to add on the side of image() |
| powerWX2019 | GWAS power analysis |
| precMatAR1 | AR(1) |
| prettyPrintBetterSummary | Print better summary |
| pruneSnpsLd | Prune SNPs based on LD |
| pseudoR2 | Pseudo R squared |
| pve2beta | Proportion of variance explained |
| qqplotPval | Q-Q plot for p values |
| qtlrelPerChr | QTLRel per chromosome |
| quantilesBinnedSnpData | Quantiles of allelic R2 after binning |
| quantNorm | Quantile-normalize a vector of numbers to a standard normal... |
| quass | Compute the inverse of the additive relationship matrix using... |
| randPlate | Randomize plate |
| readBcftoolsCounts | Read output from bcftools counts |
| readBiomercator | Returns the genetic map contained in a BioMercator TXT file. |
| readGenoDoseFileFromBcftools | Read SNP genotypes as dosage from bcftools |
| readGenosFastphase | Read genotypes from fastPHASE |
| readGenosFimpute | Read genotypes from FImpute |
| readGenosFindhap | Read genotypes from findhap |
| readHaplosFastphase | Read haplotypes from fastPHASE |
| readOutputsFimpute | Read outputs from FImpute |
| readOutputsFindhap | Read outputs from findhap |
| readOutSTRUCTURE | STRUCTURE |
| readPlinkMendel | Read PLINK |
| readSamDict | Read SAM dict |
| readSegregJoinMap | Read genotypes for JoinMap/MapQTL |
| readVcfSubset | Read VCF |
| rearrangeInputsForAssoGenet | Plant association genetics |
| recodeGenosMinorSnpAllele | Minor allele frequencies |
| recodeIntoDominant | SNP genotypes |
| reformatGenoClasses | Convert genotypes |
| regplot | Scatter plot with regression lines |
| removeFileExtension | File |
| renameVcfSamples | Rename VCF samples |
| requireNamespaces | Namespaces |
| rhoWX2019 | GWAS power analysis |
| rmatnorm | Matrix-variate Normal distribution |
| rmse | Root mean squared error |
| rngVcf2df | Convert ranges to data.frame |
| runCarthagene | Run a CarthaGene command |
| runFastphase | Genotype imputation via fastPHASE |
| runFimpute | Genotype imputation via FImpute |
| runFindhap | Genotype imputation via findhap |
| sampleWX2019 | GWAS power analysis |
| segSites2allDoses | Site frequency spectrum |
| segSites2snpCoords | Site frequency spectrum |
| seqIdStartEnd2GRanges | Make GRanges |
| setGt2Na | Set GT to NA |
| setJoinMapPhasesFromParentalLinkGroups | Genotype coding |
| setupQtlCrossObject | Set-up a R/qtl "cross" object |
| significantTests | Multiple tests correction |
| SIMQTL | QTL detection by SIM |
| simulAnimalModel | Animal model |
| simulAr1Ar1 | AR1xAR1 simulation |
| simulBslmm | BSLMM |
| simulBvsr | BVSR |
| simulCoalescent | Coalescent with recombination |
| simulGeneralisedLogistic | Generalised logistic growth (Richards' curve) |
| simulGenosDose | Genotypes |
| simulLogistic | Logistic growth |
| simulRefAltSnpAlleles | SNP alleles |
| simulRefseqCompatibleWithVcf | Fasta file |
| simulSnpEffectsTraits12 | Simul breeding game |
| simulTrait3 | Simul breeding game |
| simulTraits12 | Simul breeding game |
| snpCoordsDf2Gr | SNP coordinates from data frame to GRanges |
| solveMme | Solve MME |
| sortVcfFile | Sort a VCF file |
| splitGenomesTrainTest | Genomes |
| stanAM | Animal model (univariate) |
| stanAMwriteModel | Animal model (univariate) |
| statsAllPairAligns | Extract statistics from all pairwise alignments |
| statsStrongAssign | Genetic clustering |
| stopIfNotValidGenosDose | Genotypes |
| stopIfNotValidHaplos | Haplotypes |
| structure2clumpp | STRUCTURE to CLUMPP |
| subsetDiffHaplosWithinParent | Haplotypes |
| subsetPedigree | Subset a pedigree |
| subsetVcfOnAllelicity | Parse VCF |
| summarizeLd | Pairwise linkage disequilibrium |
| summarizeLdPerChr | Pairwise linkage disequilibrium |
| summaryFasta | Fasta file |
| summaryMcmcChain | MCMC results |
| summaryVariant | Summary per variant |
| tableVcfAlt | Read VCF |
| thinSnps | Thin SNPs |
| tridiag | Tridiagonal matrix |
| updateJoinMap | JoinMap format |
| varqual2summary | Summary per variant |
| vcf2dosage | Convert VCF to dose |
| vcf2genoClasses | Convert VCF to genotypic classes |
| writeCartagene | Genotype coding |
| writeGenMapJoinMap | Write genetic map for JoinMap/MapQTL |
| writeGenosFimpute | Write SNP genotypes for FImpute |
| writeGenosFindhap | Write SNP genotypes for findhap |
| writeInputsFastphase | Write inputs for fastPHASE |
| writeInputsFimpute | Write inputs for FImpute |
| writeInputsFindhap | Write inputs for findhap |
| writePedFileFimpute | Write pedigree for FImpute |
| writePedFileFindhap | Write pedigree for findhap |
| writePhenoJoinMap | Write phenotypes for JoinMap/MapQTL |
| writeSegregJoinMap | Write genotypes for JoinMap/MapQTL |
| writeSnpInfoFimpute | Write SNP information for FImpute |
| writeSnpInfoFindhap | Write SNP information for findhap |
