Man pages for wtaoyang/ABSSeq
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
| ABSDataSet | ABSDataSet object and constructors |
| ABSSeq | Differential expression analysis based on the total counts... |
| ABSSeqlm | Differential expression analysis for complex desgin. |
| aFoldcomplexDesign | Calculate parameters for differential expression test base on... |
| callDEs | Testing the differential expression by counts difference |
| callParameter | Calculate parameters for differential expression test base on... |
| callParameterwithoutReplicates | Calculate parameters for differential expression test base on... |
| counts | Accessors for the 'counts' slot of a ABSDataSet object. |
| estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust... |
| excounts | Accessors for the 'excounts' slot of a ABSDataSet object. |
| genAFold | Calculate parameters for differential expression test base on... |
| groups | Accessors for the 'groups' slot of a ABSDataSet object. |
| LevelstoNormFC | Accessors for the 'LevelstoNormFC' slot of a ABSDataSet... |
| maxRates | Accessors for the 'maxRates' slot of a ABSDataSet object. |
| minimalDispersion | Accessors for the 'minDispersion' slot of a ABSDataSet... |
| minRates | 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. |
| paired | Accessors for the 'paired' slot of a ABSDataSet object. |
| plotDifftoBase | Plot absolute log2 fold-change against base mean of... |
| qtotalNormalized | Estimating size factors from the reads count table via... |
| ReplaceOutliersByMAD | Replacing outliers by moderated MAD |
| results | Accessor functions for the result from a ABSDataSet |
| sFactors | Accessors for the 'sizeFactor' slot of a ABSDataSet object. |
| simuN5 | Simulated study with random outliers |
