Man pages for OliverVoogd/edgeR
Empirical Analysis of Digital Gene Expression Data in R
| addPriorCount | Add a prior count |
| adjustedProfileLik | Adjusted Profile Likelihood for the Negative Binomial... |
| asdataframe | Turn a TopTags Object into a Dataframe |
| asmatrix | Turn a DGEList Object into a Matrix |
| aveLogCPM | Average Log Counts Per Million |
| 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... |
| 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 |
| DGEExact-class | differential expression of Digital Gene Expression data -... |
| DGEGLM-class | Digital Gene Expression Generalized Linear Model results -... |
| DGEList | DGEList Constructor |
| DGEList-class | Digital Gene Expression data - class |
| DGELRT-class | Digital Gene Expression Likelihood Ratio Test data and... |
| dglmStdResid | Plot Mean-Variance Relationship in DGE Data Using... |
| diffSpliceDGE | Test for Differential Exon Usage |
| dim | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM,... |
| dimnames | 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... |
| 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... |
| estimateDisp | Estimate Common, Trended and Tagwise Negative Binomial... |
| 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... |
| estimateGLMTagwiseDisp | Empirical Bayes Tagwise Dispersions for Negative Binomial... |
| 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... |
| 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 |
| glmQLFTest | Genewise Negative Binomial Generalized Linear Models with... |
| glmTreat | Test for Differential Expression Relative to a Threshold |
| goana | Gene Ontology or KEGG Analysis of Differentially Expressed... |
| gof | Goodness of Fit Tests for Multiple GLM Fits |
| goodTuring | Good-Turing Frequency Estimation |
| head | Return the First to Last Part of a Data Object |
| loessByCol | Locally Weighted Mean By Column |
| makeCompressedMatrix | makeCompressedMatrix |
| maPlot | Plots Log-Fold Change versus Log-Concentration (or, M versus... |
| maximizeInterpolant | Maximize a function given a table of values by spline... |
| maximizeQuadratic | Maximize a function given a table of values by quadratic... |
| meanvar | Explore the Mean-Variance Relationship for DGE Data |
| mglm | Fit Negative Binomial Generalized Linear Models to Multiple... |
| modelMatrixMeth | Construct Design Matrix for edgeR Analysis of Methylation... |
| 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... |
| plotBCV | Plot Biological Coefficient of Variation |
| plotExonUsage | Create a Plot of Exon Usage from Exon-Level Count Data |
| plotMD | Mean-Difference Plot of Count Data |
| plotMDS.DGEList | Multidimensional scaling plot of distances between digital... |
| plotQLDisp | Plot the quasi-likelihood dispersion |
| plotSmear | Smear plot |
| plotSpliceDGE | Differential splicing plot |
| predFC | Predictive log-fold changes |
| processAmplicons | Process raw fastq data from pooled genetic sequencing screens |
| q2qnbinom | Quantile to Quantile Mapping between Negative-Binomial... |
| 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... |
| romer.DGEList | Rotation Gene Set Enrichment for Digital Gene Expression Data |
| rowsum | Sum Over Groups of Genes |
| scaleOffset | Scale offsets |
| SE2DGEList | SummarizedExperiment to DGEList |
| spliceVariants | Identify Genes with Splice Variants |
| splitIntoGroups | Split the Counts or Pseudocounts from a DGEList Object... |
| 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... |
| weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta |
| WLEB | Weighted Likelihood Empirical Bayes |
| zscoreNBinom | Z-score Equivalents of Negative Binomial Deviate |
