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.data.frame.TopTags   Turn a TopTags Object into a Dataframe
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
cpm                     Calculate Counts per Million from DGEList or
                        Matrix Object
cutWithMinN             Cut numeric vector into non-empty intervals
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
estimateCommonDisp      Estimates the Negative Binomial Common
                        Dispersion by Maximizing the Negative Binomial
                        Conditional Common Likelihood
estimateExonGenewiseDisp
                        Estimate Genewise Dispersions from Exon-Level
                        Count Data
estimateGLMCommonDisp   Estimate Common Dispersion for Negative
                        Binomial GLMs
estimateGLMTagwiseDisp
                        Estimate Empirical Bayes Tagwise Dispersions
                        for Negative Binomial GLMs
estimateGLMTrendedDisp
                        Estimate Trended Dispersion for Negative
                        Binomial GLMs
estimatePs              Estimate Expression Levels
estimateSmoothing       Estimate the Prior Weight for Tagwise
                        Dispersions
estimateTagwiseDisp     Estimate Empirical Bayes Tagwise Dispersion
                        Values
exactTest               Exact Tests for Differences between Two Groups
                        of Negative-Binomial Counts
expandAsMatrix          expandAsMatrix
getCounts               Extract Specified Component of a DGEList Object
getPriorN               Get a Recommended Value for Prior N 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
plotExonUsage           Create a Plot of Exon Usage from Exon-Level
                        Count Data
plotMDS.DGEList         Multidimensional scaling plot of digital gene
                        expression profiles
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
spliceVariants          Identify Genes with Splice Variants
splitIntoGroups         Split the Counts or Pseudocounts from a DGEList
                        Object According To Group
subsetting              Subset DGEList, DGEGLM, 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
