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

## Documentation for package ‘ABSSeq’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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