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 WLEB Calculate Weighted Likelihood Empirical Bayes Estimates adjustedProfileLik Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter as.data.frame.TopTags Turn a TopTags Object into a Dataframe as.matrix.DGEList Turn a DGEList Object into a Matrix aveLogCPM Average Log Counts Per Million binMeanVar Explore the mean-variance relationship for DGE data binomTest Exact Binomial Tests for Comparing Two Digital Libraries calcNormFactors Calculate Normalization Factors to Align Columns of a Count Matrix camera.DGEList Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation commonCondLogLikDerDelta Conditional Log-Likelihoods in Terms of Delta condLogLikDerSize Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries cpm Counts per Million or Reads per Kilobase per Million 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 diffSpliceDGE Test for Differential Exon Usage dim.DGEList Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object dimnames.DGEList Retrieve the Dimension Names of a DGE Object dispBinTrend Estimate Dispersion Trend by Binning for NB GLMs dispCoxReid Estimate Common Dispersion for Negative Binomial GLMs dispCoxReidInterpolateTagwise Estimate Genewise Dispersion for Negative Binomial GLMs by Cox-Reid Adjusted Profile Likelihood dispCoxReidSplineTrend Estimate Dispersion Trend for Negative Binomial GLMs dropEmptyLevels Drop Levels of a Factor that Never Occur edgeR-package Empirical analysis of digital gene expression data in R edgeRUsersGuide View edgeR User's Guide equalizeLibSizes Equalize Library Sizes by Quantile-to-Quantile Normalization estimateCommonDisp Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood estimateDisp Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes estimateExonGenewiseDisp Estimate Genewise Dispersions from Exon-Level Count Data estimateGLMCommonDisp Estimate Common Dispersion for Negative Binomial GLMs estimateGLMRobustDisp Empirical Robust Bayes Tagwise Dispersions for Negative Binomial GLMs using Observation Weights estimateGLMTagwiseDisp Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs estimateGLMTrendedDisp Estimate Trended Dispersion for Negative Binomial GLMs estimateTagwiseDisp Estimate Empirical Bayes Tagwise Dispersion Values estimateTrendedDisp Estimate Empirical Bayes Trended 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 Genewise Negative Binomial Generalized Linear Models glmQLFit Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests glmTreat Test for Differential Expression Relative to a Threshold goana.DGELRT Gene Ontology or KEGG Analysis of Differentially Expressed Genes gof Goodness of Fit Tests for Multiple GLM Fits goodTuring Good-Turing Frequency Estimation loessByCol Locally Weighted Mean By Column 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. maximizeQuadratic Maximize a function given a table of values by quadratic interpolation. mglm Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions movingAverageByCol Moving Average Smoother of Matrix Columns nbinomDeviance Negative Binomial Deviance normalizeChIPtoInput Normalize ChIP-Seq Read Counts to Input and Test for Enrichment plotBCV Plot Biological Coefficient of Variation plotExonUsage Create a Plot of Exon Usage from Exon-Level Count Data plotMD.DGEList Mean-Difference Plot of Count Data plotMDS.DGEList Multidimensional scaling plot of distances between digital gene expression profiles plotQLDisp Plot the quasi-likelihood dispersion plotSmear Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data plotSpliceDGE Differential splicing plot predFC Predictive log-fold changes processAmplicons Process raw data from pooled genetic sequencing screens q2qnbinom Quantile to Quantile Mapping between Negative-Binomial Distributions readDGE Read and Merge a Set of Files Containing Count Data roast.DGEList Rotation Gene Set Tests for Digital Gene Expression Data romer.DGEList Rotation Gene Set Tests for Digital Gene Expression 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 sumTechReps Sum Over Replicate Samples systematicSubset Take a systematic subset of indices. thinCounts Binomial or Multinomial Thinning of Counts topSpliceDGE Top table of differentially spliced genes or exons topTags Table of the Top Differentially Expressed Tags validDGEList Check for Valid DGEList object weightedCondLogLikDerDelta Weighted Conditional Log-Likelihood in Terms of Delta zscoreNBinom Z-score Equivalents of Negative Binomial Deviate