DGEExact-class          differential expression of Digital Gene
                        Expression data - class
DGEGLM-class            Digital Gene Expression Generalized Linear
                        Model results - class
DGELRT-class            Digital Gene Expression Likelihood Ratio Test
                        data and results - class
DGEList                 DGEList Constructor
DGEList-class           Digital Gene Expression data - class
Tu102                   Raw Data for Several SAGE Libraries from the
                        Zhang 1997 Science Paper.
adjustedProfileLik      Compute Cox-Reid Adjusted Profile Likelihood
                        for Negative Binomial GLMs
approx.expected.info    Approximate Expected Information (Fisher
                        Information)
as.matrix.DGEList       Turn a DGEList Object into a Matrix
betaApproxNBTest        An Approximate Exact Test for Differences
                        between Two Negative Binomial Groups
binCMLDispersion        Estimate Common Dispersion for Negative
                        Binomial GLMs in Bins of Genes Sorted by
                        Overall Abundance
binMeanVar              Explore the mean-variance relationship for DGE
                        data
binomTest               Exact Binomial Tests for Comparing Two Digital
                        Libraries
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
decideTestsDGE          Multiple Testing Across Genes and Contrasts
dglmStdResid            Visualize the mean-variance relationship in DGE
                        data using standardized residuals
dim.DGEList             Retrieve the Dimensions of a DGEList, DGEExact,
                        DGEGLM, DGELRT or TopTags Object
dimnames.DGEList        Retrieve the Dimension Names of a DGEList
                        Object
dispBinTrend            Estimate Dispersions with an
                        Abundance-Dependent Trend for Negative Binomial
                        GLMs
dispCoxReid             Estimate Common Dispersion for Negative
                        Binomial GLMs
dispCoxReidInterpolateTagwise
                        Estimate Tagwise Dispersion for Negative
                        Binomial GLMs by Cox-Reid Adjusted Profile
                        Likelihood
dispCoxReidSplineTrend
                        Estimate Dispersion Trend for Negative Binomial
                        GLMs
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
estimateCRDisp          Estimate Negative Binomial Dispersion By
                        Cox-Reid Adjusted Profile Likelihood (Obsolete)
estimateCommonDisp      Estimates the Negative Binomial Common
                        Dispersion by Maximizing the Negative Binomial
                        Conditional Common Likelihood
estimateGLMCommonDisp   Estimate Common Dispersion for Negative
                        Binomial GLMs
estimateGLMTagwiseDisp
                        Estimate Tagwise Dispersions for Negative
                        Binomial GLMs
estimateGLMTrendedDisp
                        Estimate Trended Dispersion for Negative
                        Binomial GLMs
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
expandAsMatrix          expandAsMatrix
getCounts               Extract Table of Counts from DGEList Object
getOffsets              Extract Vector of Offsets from DGEList Object
glmFit                  Fit negative binomial generalized linear model
                        for each transcript
gof                     Goodness of Fit Tests for Multiple GLM Fits
goodTuring              Good-Turing Frequency Estimation
logLikDerP              Log-Likelihood for Proportion
maPlot                  Plots Log-Fold Change versus Log-Concentration
                        (or, M versus A) for Count Data
maximizeInterpolant     Maximize a function given a table of values by
                        spline interpolation.
mglm                    Fit Negative Binomial Generalized Linear Model
                        to Multiple Response Vectors
movingAverageByCol      Moving Average Smoother of Matrix Columns
plotMDS.dge             Multidimensional scaling plot of digital gene
                        expression 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
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, DGEExact and DGELRT Objects
systematicSubset        Take a systematic subset of indices.
thinCounts              Binomial Thinning of Counts
topTags                 Table of the Top Differentially Expressed Tags
weightedComLik          Weighted Common Log-Likelihood
weightedCondLogLikDerDelta
                        Weighted Conditional Log-Likelihood in Terms of
                        Delta
