# OUTRIDER - OUTlier in RNA-Seq fInDER

## Documentation for package ‘OUTRIDER’ version 1.31.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

aberrant | Number of aberrant events
aberrant-method | Number of aberrant events
computeGeneLength | Extracting the gene length from annotations
computeLatentSpace | Extracting the latent space
computePvalues | Calculate P-values
computePvalues-method | Calculate P-values
computeZscores | Z score computation
computeZscores-method | Z score computation
controlForConfounders | Autoencoder function to correct for confounders.
counts | Accessors for the 'counts' slot of an OutriderDataSet object.
counts-method | Accessors for the 'counts' slot of an OutriderDataSet object.
counts<--method | Accessors for the 'counts' slot of an OutriderDataSet object.
dispersion, | Getter/Setter functions
dispersions | Getter/Setter functions
dispersions-method | Getter/Setter functions
estimateBestQ | Find the optimal encoding dimension
estimateBestQ, | Find the optimal encoding dimension
estimateSizeFactors | SizeFactors accessor and estimation function
estimateSizeFactors-method | SizeFactors accessor and estimation function
filterExpression | Filter expression
filterExpression-method | Filter expression
findInjectZscore | Find the optimal encoding dimension
fit | Fit the negative binomial distribution
fit.OutriderDataSet | Fit the negative binomial distribution
fpkm | Calculate FPM and FPKM values
fpm | Calculate FPM and FPKM values
getBestQ | Getter/Setter functions
getter_setter_functions | Getter/Setter functions
makeExampleOutriderDataSet | Create example data sets for OUTRIDER
normalizationFactors | Accessor functions for the normalization factors in an OutriderDataSet object.
normalizationFactors-method | Accessor functions for the normalization factors in an OutriderDataSet object.
normalizationFactors<--method | Accessor functions for the normalization factors in an OutriderDataSet object.
OUTRIDER | OUTRIDER - Finding expression outlier events
OutriderDataSet | OutriderDataSet class and constructors
OutriderDataSet-class | OutriderDataSet class and constructors
padj | Getter/Setter functions
padj, | Getter/Setter functions
plotAberrantPerSample | Visualization functions for OUTRIDER
plotAberrantPerSample-method | Visualization functions for OUTRIDER
plotCountCorHeatmap | Visualization functions for OUTRIDER
plotCountCorHeatmap-method | Visualization functions for OUTRIDER
plotCountGeneSampleHeatmap | Visualization functions for OUTRIDER
plotDispEsts | Visualization functions for OUTRIDER
plotDispEsts-method | Visualization functions for OUTRIDER
plotEncDimSearch | Visualization functions for OUTRIDER
plotEncDimSearch-method | Visualization functions for OUTRIDER
plotExpectedVsObservedCounts | Visualization functions for OUTRIDER
plotExpressedGenes | Visualization functions for OUTRIDER
plotExpressionRank | Visualization functions for OUTRIDER
plotFPKM | Visualization functions for OUTRIDER
plotFunction | Visualization functions for OUTRIDER
plotFunctions | Visualization functions for OUTRIDER
plotManhattan | Visualization functions for OUTRIDER
plotManhattan-method | Visualization functions for OUTRIDER
plotPowerAnalysis | Visualization functions for OUTRIDER
plotQQ | Visualization functions for OUTRIDER
plotQQ-method | Visualization functions for OUTRIDER
plotSizeFactors | Visualization functions for OUTRIDER
plotVolcano | Visualization functions for OUTRIDER
plotVolcano-method | Visualization functions for OUTRIDER
pValue | Getter/Setter functions
pValue, | Getter/Setter functions
results | Accessor function for the 'results' object in an OutriderDataSet object.
results-method | Accessor function for the 'results' object in an OutriderDataSet object.
sampleExclusionMask | Sample exclusion
sampleExclusionMask, | Sample exclusion
sampleExclusionMask<- | Sample exclusion
sizeFactors | SizeFactors accessor and estimation function
sizeFactors-method | SizeFactors accessor and estimation function
sizeFactors<- | SizeFactors accessor and estimation function
sizeFactors<--method | SizeFactors accessor and estimation function
theta | Getter/Setter functions
theta, | Getter/Setter functions
zScore | Getter/Setter functions
zScore, | Getter/Setter functions
`sampleExclusionMask<-` | Sample exclusion