Man pages for edgeR
Empirical Analysis of Digital Gene Expression Data in R

addPriorCountAdd a prior count
adjustedProfileLikAdjusted Profile Likelihood for the Negative Binomial...
asdataframeTurn a TopTags Object into a Dataframe
asmatrixTurn a DGEList Object into a Matrix
aveLogCPMAverage Log Counts Per Million
binomTestExact Binomial Tests for Comparing Two Digital Libraries
calcNormFactorsLibrary Size Normalization
camera.DGEListCompetitive Gene Set Tests for Digital Gene Expression Data
catchSalmonProcess Kallisto or Salmon Output
cbindCombine DGEList Objects
commonCondLogLikDerDeltaConditional Log-Likelihoods in Terms of Delta
condLogLikDerSizeConditional Log-Likelihood of the Dispersion for a Single...
cpmCounts per Million or Reads per Kilobase per Million
cutWithMinNCut numeric vector into non-empty intervals
decidetestsDGEMultiple Testing Across Genes and Contrasts
DGEExact-classdifferential expression of Digital Gene Expression data -...
DGEGLM-classDigital Gene Expression Generalized Linear Model results -...
DGEListDGEList Constructor
DGEList-classDigital Gene Expression data - class
DGELRT-classDigital Gene Expression Likelihood Ratio Test data and...
dglmStdResidPlot Mean-Variance Relationship in DGE Data Using...
diffSpliceDGETest for Differential Exon Usage
dimRetrieve the Dimensions of a DGEList, DGEExact, DGEGLM,...
dimnamesRetrieve the Dimension Names of a DGE Object
dispBinTrendEstimate Dispersion Trend by Binning for NB GLMs
dispCoxReidEstimate Common Dispersion for Negative Binomial GLMs
dispCoxReidInterpolateTagwiseEstimate Genewise Dispersion for Negative Binomial GLMs by...
dispCoxReidSplineTrendEstimate Dispersion Trend for Negative Binomial GLMs
dropEmptyLevelsDrop Levels of a Factor that Never Occur
edgeR-packageEmpirical analysis of digital gene expression data in R
edgeRUsersGuideView edgeR User's Guide
effectiveLibSizesEffective Library Sizes
equalizeLibSizesEqualize Library Sizes by Quantile-to-Quantile Normalization
estimateCommonDispEstimate Common Negative Binomial Dispersion by Conditional...
estimateDispEstimate Common, Trended and Tagwise Negative Binomial...
estimateExonGenewisedispEstimate Genewise Dispersions from Exon-Level Count Data
estimateGLMCommonDispEstimate Common Dispersion for Negative Binomial GLMs
estimateGLMRobustDispEmpirical Robust Bayes Tagwise Dispersions for Negative...
estimateGLMTagwiseDispEmpirical Bayes Tagwise Dispersions for Negative Binomial...
estimateGLMTrendedDispEstimate Trended Dispersion for Negative Binomial GLMs
estimateTagwiseDispEstimate Empirical Bayes Tagwise Dispersion Values
estimateTrendedDispEstimate Empirical Bayes Trended Dispersion Values
exactTestExact Tests for Differences between Two Groups of...
filterByExprFilter Genes By Expression Level
getCountsExtract Specified Component of a DGEList Object
getPriorNGet a Recommended Value for Prior N from DGEList Object
giniGini dispersion index
glmfitGenewise Negative Binomial Generalized Linear Models
glmQLFTestGenewise Negative Binomial Generalized Linear Models with...
glmTreatTest for Differential Expression Relative to a Threshold
goanaGene Ontology or KEGG Analysis of Differentially Expressed...
gofGoodness of Fit Tests for Multiple GLM Fits
goodTuringGood-Turing Frequency Estimation
headReturn the First to Last Part of a Data Object
loessByColLocally Weighted Mean By Column
maPlotPlots Log-Fold Change versus Log-Concentration (or, M versus...
maximizeInterpolantMaximize a function given a table of values by spline...
maximizeQuadraticMaximize a function given a table of values by quadratic...
meanvarExplore the Mean-Variance Relationship for DGE Data
mglmFit Negative Binomial Generalized Linear Models to Multiple...
modelMatrixMethConstruct Design Matrix for edgeR Analysis of Methylation...
movingAverageByColMoving Average Smoother of Matrix Columns
nbinomDevianceNegative Binomial Deviance
nbinomUnitDevianceNegative Binomial Unit Deviance
nearestReftoXFind Nearest Element of Reference for each Element of X
nearestTSSFind Nearest Transcriptional Start Site
normalizeChIPtoInputNormalize ChIP-Seq Read Counts to Input and Test for...
plotBCVPlot Biological Coefficient of Variation
plotExonUsageCreate a Plot of Exon Usage from Exon-Level Count Data
plotMDMean-Difference Plot of Count Data
plotMDS.DGEListMultidimensional scaling plot of distances between digital...
plotQLDispPlot the quasi-likelihood dispersion
plotSmearSmear plot
plotSpliceDGEDifferential splicing plot
predFCPredictive log-fold changes
processAmpliconsProcess raw fastq data from pooled genetic sequencing screens
q2qnbinomQuantile to Quantile Mapping between Negative-Binomial...
read10XRead 10X Genomics Files
readBismark2DGERead Bismark Coverage Files
readDGERead and Merge a Set of Files Containing Count Data
roast.DGEListSelf-contained Gene Set Tests for Digital Gene Expression...
romer.DGEListRotation Gene Set Enrichment for Digital Gene Expression Data
rowsumSum Over Groups of Genes
scaleOffsetScale offsets
SE2DGEListSummarizedExperiment to DGEList
spliceVariantsIdentify Genes with Splice Variants
splitIntoGroupsSplit the Counts or Pseudocounts from a DGEList Object...
subsettingSubset DGEList, DGEGLM, DGEExact and DGELRT Objects
sumTechRepsSum Over Replicate Samples
systematicSubsetTake a systematic subset of indices.
thinCountsBinomial or Multinomial Thinning of Counts
topSpliceDGETop table of differentially spliced genes or exons
topTagsTable of the Top Differentially Expressed Genes/Tags
validDGEListCheck for Valid DGEList object
voomLmFitApply voom-lmFit Pipeline While Accounting for Loss of...
weightedCondLogLikDerDeltaWeighted Conditional Log-Likelihood in Terms of Delta
WLEBWeighted Likelihood Empirical Bayes
zscoreNBinomZ-score Equivalents of Negative Binomial Deviate
edgeR documentation built on Jan. 16, 2021, 2:03 a.m.