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| ABSDataSet | ABSDataSet object and constructors |
| ABSDataSet-class | ABSDataSet object and constructors |
| ABSSeq | Differential expression analysis based on the total counts difference. |
| ABSSeqlm | Differential expression analysis for complex desgin. |
| aFoldcomplexDesign | Calculate parameters for differential expression test base on absolute counts differences |
| callDEs | Testing the differential expression by counts difference |
| callParameter | Calculate parameters for differential expression test base on absolute counts differences |
| callParameterwithoutReplicates | Calculate parameters for differential expression test base on absolute counts differences without replicates |
| counts | Accessors for the 'counts' slot of a ABSDataSet object. |
| counts-method | Accessors for the 'counts' slot of a ABSDataSet object. |
| counts<- | Accessors for the 'counts' slot of a ABSDataSet object. |
| counts<--method | Accessors for the 'counts' slot of a ABSDataSet object. |
| estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust regression. |
| excounts | Accessors for the 'excounts' slot of a ABSDataSet object. |
| excounts-method | Accessors for the 'excounts' slot of a ABSDataSet object. |
| excounts<- | Accessors for the 'excounts' slot of a ABSDataSet object. |
| excounts<--method | Accessors for the 'excounts' slot of a ABSDataSet object. |
| genAFold | Calculate parameters for differential expression test base on absolute counts differences |
| groups | Accessors for the 'groups' slot of a ABSDataSet object. |
| groups-method | Accessors for the 'groups' slot of a ABSDataSet object. |
| groups<- | Accessors for the 'groups' slot of a ABSDataSet object. |
| groups<--method | Accessors for the 'groups' slot of a ABSDataSet object. |
| LevelstoNormFC | Accessors for the 'LevelstoNormFC' slot of a ABSDataSet object. |
| LevelstoNormFC-method | Accessors for the 'LevelstoNormFC' slot of a ABSDataSet object. |
| LevelstoNormFC<- | Accessors for the 'LevelstoNormFC' slot of a ABSDataSet object. |
| LevelstoNormFC<--method | Accessors for the 'LevelstoNormFC' slot of a ABSDataSet object. |
| maxRates | Accessors for the 'maxRates' slot of a ABSDataSet object. |
| maxRates-method | Accessors for the 'maxRates' slot of a ABSDataSet object. |
| maxRates<- | Accessors for the 'maxRates' slot of a ABSDataSet object. |
| maxRates<--method | Accessors for the 'maxRates' slot of a ABSDataSet object. |
| minimalDispersion | Accessors for the 'minDispersion' slot of a ABSDataSet object. |
| minimalDispersion-method | Accessors for the 'minDispersion' slot of a ABSDataSet object. |
| minimalDispersion<- | Accessors for the 'minDispersion' slot of a ABSDataSet object. |
| minimalDispersion<--method | Accessors for the 'minDispersion' slot of a ABSDataSet object. |
| minRates | Accessors for the 'minRates' slot of a ABSDataSet object. |
| minRates-method | Accessors for the 'minRates' slot of a ABSDataSet object. |
| minRates<- | Accessors for the 'minRates' slot of a ABSDataSet object. |
| minRates<--method | Accessors for the 'minRates' slot of a ABSDataSet object. |
| normalFactors | Estimating size factors from the reads count table |
| normMethod | Accessors for the 'normMethod' slot of a ABSDataSet object. |
| normMethod-method | Accessors for the 'normMethod' slot of a ABSDataSet object. |
| normMethod<- | Accessors for the 'normMethod' slot of a ABSDataSet object. |
| normMethod<--method | Accessors for the 'normMethod' slot of a ABSDataSet object. |
| paired | Accessors for the 'paired' slot of a ABSDataSet object. |
| paired-method | Accessors for the 'paired' slot of a ABSDataSet object. |
| paired<- | Accessors for the 'paired' slot of a ABSDataSet object. |
| paired<--method | Accessors for the 'paired' slot of a ABSDataSet object. |
| plotDifftoBase | Plot absolute log2 fold-change against base mean of expression |
| qtotalNormalized | Estimating size factors from the reads count table via ranking |
| ReplaceOutliersByMAD | Replacing outliers by moderated MAD |
| results | Accessor functions for the result from a ABSDataSet |
| results-method | Accessor functions for the result from a ABSDataSet |
| sFactors | Accessors for the 'sizeFactor' slot of a ABSDataSet object. |
| sFactors-method | Accessors for the 'sizeFactor' slot of a ABSDataSet object. |
| sFactors<- | Accessors for the 'sizeFactor' slot of a ABSDataSet object. |
| sFactors<--method | Accessors for the 'sizeFactor' slot of a ABSDataSet object. |
| simuN5 | Simulated study with random outliers |
| SumInfo-class | ABSDataSet object and constructors |
| [[<--method | ABSDataSet object and constructors |