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 SE2DGEList SummarizedExperiment to DGEList WLEB Weighted Likelihood Empirical Bayes addPriorCount Add a prior count adjustedProfileLik Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter as.data.frame.DGEList 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 Library Size Normalization camera.DGEList Competitive Gene Set Tests for Digital Gene Expression Data catchSalmon Process Kallisto or Salmon Output cbind Combine DGEList Objects 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 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 effectiveLibSizes Effective Library Sizes 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 featureCounts2DGEList Convert featureCounts object to a DGEList filterByExpr Filter Genes By Expression Level getCounts Extract Specified Component of a DGEList Object getPriorN Get a Recommended Value for Prior N from DGEList Object gini Gini dispersion index 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 head.DGEList Return the First to Last Part of a Data Object loessByCol Locally Weighted Mean By Column maPlot Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data makeCompressedMatrix makeCompressedMatrix 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 Models to Multiple Response Vectors: Low Level Functions modelMatrixMeth Construct Design Matrix for edgeR Analysis of Methylation Count Data movingAverageByCol Moving Average Smoother of Matrix Columns nbinomDeviance Negative Binomial Deviance nbinomUnitDeviance Negative Binomial Unit Deviance nearestReftoX Find Nearest Element of Reference for each Element of X nearestTSS Find Nearest Transcriptional Start Site 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 plotMeanVar2 Plot Mean-Variance Relationship in DGE Data Using Standardized Residuals plotQLDisp Plot the quasi-likelihood dispersion plotSmear Smear plot plotSpliceDGE Differential splicing plot predFC Predictive log-fold changes processAmplicons Process FASTQ files from pooled genetic sequencing screens q2qnbinom Quantile to Quantile Mapping between Negative-Binomial Distributions read10X Read 10X Genomics Files readBismark2DGE Read Bismark Coverage Files readDGE Read and Merge a Set of Files Containing Count Data roast.DGEList Self-contained Gene Set Tests for Digital Gene Expression Data romer.DGEList Rotation Gene Set Enrichment for Digital Gene Expression Data rowsum.DGEList Sum Over Groups of Genes scaleOffset Scale offsets 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 Genes/Tags validDGEList Check for Valid DGEList object voomLmFit Apply voom-lmFit Pipeline While Accounting for Loss of Residual DF Due to Exact Zeros weightedCondLogLikDerDelta Weighted Conditional Log-Likelihood in Terms of Delta zscoreNBinom Z-score Equivalents of Negative Binomial Deviate