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| 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 |