DGEList                 DGEList Constructor
DGEList-class           Digital Gene Expression data - class
EBList-class            Differential Expression of Digital Gene
                        Expression data - class
Tu102                   Raw Data for Several SAGE Libraries from the
                        Zhang 1997 Science Paper.
alpha.approxeb          Estimate the Prior Weight, Alpha
approx.expected.info    Approximate Expected Information (Fisher
                        Information)
calcNormFactors         Calculates Normalization Factors for a Matrix
                        of Count Data
commonCondLogLikDerDelta
                        Conditional Log-Likelihoods in Terms of Delta
condLogLikDerDelta      Conditional Log-Likelihood in Terms of Delta
condLogLikDerSize       Log-Likelihood of the Common Dispersion for a
                        Single Equalized Group
de4DGE                  Compute Moderated Differential Expression
                        Scores for Digital Gene Expression (DGE) Data
de4DGEList-class        differential expression for Digital Gene
                        Expression data - class
deDGE                   Compute Moderated Differential Expression
                        Scores for Digital Gene Expression (DGE) Data
deDGEList-class         differential expression of Digital Gene
                        Expression data - class
edgeR-package           Empirical analysis of digital gene expression
                        data in R
equalizeLibSizes        Quantile Adjustment to Equalize Library Sizes
                        for a Fixed Value of the Dispersion Parameter
estimateCommonDisp      Estimates the Negative Binomial Common
                        Dispersion by Maximizing the Negative Binomial
                        Conditional Common Likelihood
estimateDispIter        Normalizes a Dataset Using Quantile Adjustment
                        and Iteratively Estimates the Dispersion
                        Parameter
estimatePs              Estimate Expression Levels
estimateSmoothing       Estimate the Prior Weight
estimateTagwiseDisp     Maximizes the Negative Binomial Weighted
                        Conditional Likelihood
exactTest               An Exact Test for Differences between Two
                        Negative Binomial Groups
findMaxD2               Maximizes the Negative Binomial Likelihood
getCounts               Extract Table of Counts from DGEList Object
interpolateHelper       Quantile Adjustment Interpolator
logLikDerP              Log-Likelihood for Proportion
maPlot                  Plots Log-Fold Change versus Log-Concentration
                        (or, M versus A) for Count Data
plotSmear               Plots log-Fold Change versus log-Concentration
                        (or, M versus A) for Count Data
q2qnbinom               Quantile to Quantile Mapping between
                        Negative-Binomial Distributions
quantileAdjust          Normalizes a Dataset by Using a Quantile
                        Adjustment
readDGE                 Read and Merge a Set of Files Containing DGE
                        Data
splitIntoGroups         Split the Counts or Pseudocounts from a DGEList
                        Object According To Group
subsetting              Subset DGEList Objects
tau2.0.objective        Objective Function for Tau2
topTags                 Table of the Top Differentially Expressed Tags
weightedCondLogLikDerDelta
                        Weighted Conditional Log-Likelihood in Terms of
                        Delta
