OUTRIDER - OUTlier in RNA-Seq fInDER

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Documentation for package ‘OUTRIDER’ version 1.16.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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	Estimation of Q
estimateSizeFactors	SizeFactors accessor and estimation function
estimateSizeFactors-method	SizeFactors accessor and estimation function
filterExpression	Filter expression
filterExpression-method	Filter expression
findEncodingDim	Find the optimal encoding dimension
findEncodingDim,	Find the optimal encoding dimension
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
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