# ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

## Documentation for package ‘ABSSeq’ version 1.62.0

- 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 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