ABSDataSet |
ABSDataSet object and constructors |
ABSDataSet-class |
ABSDataSet object and constructors |
ABSSeq |
Differential expression analysis based on the total counts difference. |
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. |
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. |
plotDifftoBase |
Plot absolute log2 fold-change against base mean of expression |
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 |