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

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Documentation for package ‘ABSSeq’ version 1.61.0

• 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