API for gagneurlab/OUTRIDER
OUTRIDER - OUTlier in RNA-Seq fInDER

Global functions
D Source code
E Source code
H Source code
OUTRIDER Man page Source code
OutriderDataSet Man page Source code
OutriderDataSet-class Man page
ZscoreMatrix Source code
`D<-` Source code
`E<-` Source code
`b<-` Source code
`pValue<-` Source code
`padj<-` Source code
`sampleExclusionMask<-` Man page Source code
`theta<-` Source code
`thetaCorrection<-` Source code
`trueCounts<-` Source code
`zScore<-` Source code
aberrant Man page
aberrant,OutriderDataSet-method Man page
aberrant.OUTRIDER Source code
autoCorrectPCA Source code
b Source code
checkCountRequirements Source code
checkFullAnalysis Source code
checkNames Source code
checkOutriderDataSet Source code
checkSizeFactors Source code
checkThetaRange Source code
compileResults.OUTRIDER Source code
computeExpressedGenes Source code
computeGeneLength Man page Source code
computeLatentSpace Man page Source code
computePvalues Man page
computePvalues,OutriderDataSet-method Man page
computeZscores Man page
computeZscores,OutriderDataSet-method Man page
controlForConfounders Man page Source code
counts Man page
counts,OutriderDataSet-method Man page
counts.OutriderDataSet Source code
counts.replace.OutriderDataSet Source code
counts<-,OutriderDataSet,matrix-method Man page
dispersion, Man page
dispersions Man page
dispersions,OutriderDataSet-method Man page
estTheta Source code
estimateBestQ Man page Source code
estimateSizeFactors Man page
estimateSizeFactors,OutriderDataSet-method Man page
estimateSizeFactors.OUTRIDER Source code
filterExp Source code
filterExpression Man page
filterExpression,OutriderDataSet-method Man page
filterExpression.OUTRIDER Source code
filterMinCounts Source code
findEncodingDim Man page Source code
findEncodingDim, Man page
findInjectZscore Man page Source code
fit Man page
fit.OutriderDataSet Man page Source code
fitAutoencoder Source code
fitNegBinom Source code
fitTheta Source code
fpkm Man page
fpm Man page
getAnnoColors Source code
getAnnoHeatmap Source code
getBestQ Man page Source code
getBestQDT Source code
getDispEstsData Source code
getGeneIndex Source code
getLossBounderyCases Source code
getNiceName Source code
getXColors Source code
getter_setter_functions Man page
gradD Source code
gradTheta Source code
gradientD Source code
gradientE Source code
gradloglikelihood Source code
ignoreAesTextWarning Source code
initAutoencoder Source code
initialSizeMu Source code
log2fc Source code
loglikelihood Source code
lossD Source code
lossDtrunc Source code
lossE Source code
lossED Source code
lossEtruncNonOutlier Source code
lossGradENonOutlier Source code
makeExampleOutriderDataSet Man page Source code
negLogLikelihoodTheta Source code
normFactors.replace.OutriderDataSet Source code
normalizationFactors Man page
normalizationFactors,OutriderDataSet-method Man page
normalizationFactors.OutriderDataSet Source code
normalizationFactors<-,OutriderDataSet,DataFrame-method Man page
normalizationFactors<-,OutriderDataSet,NULL-method Man page
normalizationFactors<-,OutriderDataSet,data.frame-method Man page
normalizationFactors<-,OutriderDataSet,matrix-method Man page
pVal Source code
pValMatrix Source code
pValue Man page Source code
pValue, Man page
padj Man page Source code
padj, Man page
padjMatrix Source code
plotAberrantPerSample Man page
plotAberrantPerSample,OutriderDataSet-method Man page
plotAberrantPerSample.OUTRIDER Source code
plotCountCorHeatmap Man page
plotCountCorHeatmap,OutriderDataSet-method Man page
plotCountCorHeatmap.OUTRIDER Source code
plotCountCorHeatmapPlotly Source code
plotCountGeneSampleHeatmap Man page Source code
plotDispEsts Man page
plotDispEsts,OutriderDataSet-method Man page
plotDispEsts.OUTRIDER Source code
plotEncDimSearch Man page
plotEncDimSearch,OutriderDataSet-method Man page
plotEncDimSearch.OUTRIDER Source code
plotExpectedVsObservedCounts Man page Source code
plotExpressedGenes Man page
plotExpressionRank Man page Source code
plotFPKM Man page Source code
plotFunction Man page
plotFunctions Man page
plotHeatmap Source code
plotPowerAnalysis Man page Source code
plotQQ Man page
plotQQ,OutriderDataSet-method Man page
plotQQ.OUTRIDER Source code
plotSizeFactors Man page
plotVolcano Man page
plotVolcano,OutriderDataSet-method Man page
plotVolcano.OUTRIDER Source code
predictC Source code
predictMatC Source code
predictMatY Source code
predictY Source code
results Man page
results,OutriderDataSet-method Man page
robustMethodOfMomentsOfTheta Source code
sampleExclusionMask Man page Source code
sampleExclusionMask, Man page
sampleExclusionMask<- Man page
sdLogScale Source code
showOutriderDataSet Source code
singleDFit Source code
sizeFactors Man page
sizeFactors,OutriderDataSet-method Man page
sizeFactors.OutriderDataSet Source code
sizeFactors.replace.OutriderDataSet Source code
sizeFactors<- Man page
sizeFactors<-,OutriderDataSet,NULL-method Man page
sizeFactors<-,OutriderDataSet,numeric-method Man page
theta Man page Source code
theta, Man page
thetaCorrection Source code
trueCounts Source code
truncLogLiklihoodD Source code
truncLogLiklihoodE Source code
updateD Source code
updateE Source code
updateLossList Source code
updateTheta Source code
validateCounts Source code
validateOutriderDataSet Source code
x Source code
zScore Man page Source code
zScore, Man page
gagneurlab/OUTRIDER documentation built on Oct. 24, 2020, 6:49 p.m.