# Empirical analysis of digital gene expression data in R

## Documentation for package ‘edgeR’ version 1.4.7

## User Guides and Package Vignettes

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## Help Pages

edgeR-package | Empirical analysis of digital gene expression data in R
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
DGEList | DGEList Constructor
DGEList-class | Digital Gene Expression data - class
EBList-class | Differential Expression of Digital Gene Expression data - class
edgeR | 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
exactTest.matrix | 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
NC1 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.
NC2 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.
plotFC | 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
q2qpois | 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
show,de4DGEList-method | differential expression for Digital Gene Expression data - class
show,deDGEList-method | differential expression of Digital Gene Expression data - class
show,EBList-method | Differential Expression of Digital Gene Expression data - class
show,TopTags-method | Table of the Top Differentially Expressed Tags
splitIntoGroups | Split the Counts or Pseudocounts from a DGEList Object According To Group
splitIntoGroupsPseudo | 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
TopTags-class | Table of the Top Differentially Expressed Tags
Tu102 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.
Tu98 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.
weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta
[.DGEList | Subset DGEList Objects
[.TopTags | Table of the Top Differentially Expressed Tags