ABSSeq: a new RNA-Seq analysis method based on absolute expression differences and generalized Poisson model

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Documentation for package ‘ABSSeq’ version 1.0.1

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ABSDataSet ABSDataSet object and constructors
ABSDataSet-class ABSDataSet object and constructors
ABSSeq Differential expression analysis based on the absolute difference.
calPara Calculate parameters for generalized Poisson test (GPTest)
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.
GPTest Testing the differential expression
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.
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 differencs
results Accessor functions for the result from a ABSDataSet
results-method Accessor functions for the result from a ABSDataSet
simuN5 Simulated study with random outliers
sizeFactors Accessors for the 'sizeFactor' slot of a ABSDataSet object.
sizeFactors-method Accessors for the 'sizeFactor' slot of a ABSDataSet object.
sizeFactors<- Accessors for the 'sizeFactor' slot of a ABSDataSet object.
sizeFactors<--method Accessors for the 'sizeFactor' slot of a ABSDataSet object.
SumInfo An S4 class that stores a string.
SumInfo-class ABSDataSet object and constructors
[[<--method ABSDataSet object and constructors