Empirical analysis of digital gene expression data in R


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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