edgeR: Empirical Analysis of Digital Gene Expression Data in R
Version 3.18.1

Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

AuthorYunshun Chen <yuchen@wehi.edu.au>, Aaron Lun <alun@wehi.edu.au>, Davis McCarthy <dmccarthy@wehi.edu.au>, Xiaobei Zhou <xiaobei.zhou@uzh.ch>, Mark Robinson <mark.robinson@imls.uzh.ch>, Gordon Smyth <smyth@wehi.edu.au>
Bioconductor views AlternativeSplicing BatchEffect Bayesian ChIPSeq Clustering Coverage DifferentialExpression DifferentialSplicing GeneExpression GeneSetEnrichment Genetics MultipleComparison Normalization QualityControl RNASeq Regression SAGE Sequencing TimeCourse Transcription
Date of publicationNone
MaintainerYunshun Chen <yuchen@wehi.edu.au>, Aaron Lun <alun@wehi.edu.au>, Mark Robinson <mark.robinson@imls.uzh.ch>, Davis McCarthy <dmccarthy@wehi.edu.au>, Gordon Smyth <smyth@wehi.edu.au>
LicenseGPL (>=2)
Version3.18.1
URL http://bioinf.wehi.edu.au/edgeR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("edgeR")

Getting started

Package overview

Popular man pages

aveLogCPM: Average Log Counts Per Million
cpm: Counts per Million or Reads per Kilobase per Million
exactTest: Exact Tests for Differences between Two Groups of...
plotMDS.DGEList: Multidimensional scaling plot of distances between digital...
plotSmear: Smear plot
subsetting: Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
topTags: Table of the Top Differentially Expressed Tags
See all...

All man pages Function index File listing

Man pages

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: Calculate Normalization Factors to Align Columns of a Count...
camera.DGEList: Competitive Gene Set Test for Digital Gene Expression Data...
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: Visualize the 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
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
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
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 Model to Multiple...
movingAverageByCol: Moving Average Smoother of Matrix Columns
nbinomDeviance: Negative Binomial Deviance
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 data from pooled genetic sequencing screens
q2qnbinom: Quantile to Quantile Mapping between Negative-Binomial...
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
scaleOffset: Scale offsets
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 Tags
validDGEList: Check for Valid DGEList object
weightedCondLogLikDerDelta: Weighted Conditional Log-Likelihood in Terms of Delta
WLEB: Calculate Weighted Likelihood Empirical Bayes Estimates
zscoreNBinom: Z-score Equivalents of Negative Binomial Deviate

Functions

DGEExact-class Man page
DGEGLM-class Man page
DGELRT-class Man page
DGEList Man page Source code
DGEList-class Man page
TopTags-class Man page
WLEB Man page Source code
[.DGEExact Man page
[.DGEGLM Man page
[.DGELRT Man page
[.DGEList Man page
[.TopTags Man page
[.compressedMatrix Man page
addCompressedMatrices Source code
addPriorCount Man page Source code
adjustedProfileLik Man page Source code
areFittedValuesZero Source code
as.data.frame.TopTags Man page Source code
as.matrix.DGEList Man page Source code
as.matrix.compressedMatrix Man page Source code
aveLogCPM Man page Source code
aveLogCPM.DGEGLM Man page Source code
aveLogCPM.DGEList Man page Source code
aveLogCPM.default Man page Source code
binMeanVar Man page Source code
binomTest Man page Source code
calcFactorQuantile Source code
calcFactorRLE Source code
calcFactorWeighted Source code
calcNormFactors Man page Source code
calcNormFactors.DGEList Man page Source code
calcNormFactors.default Man page Source code
calcNormOffsetsforChIP Man page Source code
calcResid Source code
camera.DGEList Man page Source code
comboGroups Source code
commonCondLogLikDerDelta Man page Source code
compressDispersions Source code
compressOffsets Source code
compressPrior Source code
compressWeights Source code
compressedMatrix Man page
compute_nbdeviance Source code
condLogLikDerDelta Man page Source code
condLogLikDerSize Man page Source code
cpm Man page Source code
cpm.DGEList Man page Source code
cpm.default Man page Source code
cutWithMinN Man page Source code
decideTests.DGEExact Man page
decideTests.DGELRT Man page
decideTestsDGE Man page Source code
designAsFactor Man page Source code
dglmStdResid Man page Source code
diffSpliceDGE Man page Source code
dim.DGEExact Man page
dim.DGEGLM Man page Source code
dim.DGELRT Man page Source code
dim.DGEList Man page Source code
dim.TopTags Man page
dimnames.DGEExact Man page
dimnames.DGEGLM Man page Source code
dimnames.DGELRT Man page
dimnames.DGEList Man page Source code
dimnames.TopTags Man page Source code
dimnames<-.DGEExact Man page
dimnames<-.DGEGLM Man page
dimnames<-.DGELRT Man page
dimnames<-.DGEList Man page
dispBinTrend Man page Source code
dispCoxReid Man page Source code
dispCoxReidInterpolateTagwise Man page Source code
dispCoxReidPowerTrend Man page Source code
dispCoxReidSplineTrend Man page Source code
dispDeviance Man page Source code
dispPearson Man page Source code
dropEmptyLevels Man page Source code
edgeR Man page
edgeR-package Man page
edgeRUsersGuide Man page Source code
equalizeLibSizes Man page Source code
equalizeLibSizes.DGEList Man page Source code
equalizeLibSizes.default Man page Source code
estimateCommonDisp Man page Source code
estimateCommonDisp.DGEList Man page Source code
estimateCommonDisp.default Man page Source code
estimateDisp Man page Source code
estimateDisp.DGEList Man page Source code
estimateDisp.default Man page Source code
estimateExonGenewiseDisp Man page Source code
estimateGLMCommonDisp Man page Source code
estimateGLMCommonDisp.DGEList Man page Source code
estimateGLMCommonDisp.default Man page Source code
estimateGLMRobustDisp Man page Source code
estimateGLMTagwiseDisp Man page Source code
estimateGLMTagwiseDisp.DGEList Man page Source code
estimateGLMTagwiseDisp.default Man page Source code
estimateGLMTrendedDisp Man page Source code
estimateGLMTrendedDisp.DGEList Man page Source code
estimateGLMTrendedDisp.default Man page Source code
estimateTagwiseDisp Man page Source code
estimateTagwiseDisp.DGEList Man page Source code
estimateTagwiseDisp.default Man page Source code
estimateTrendedDisp Man page Source code
estimateTrendedDisp.DGEList Man page Source code
estimateTrendedDisp.default Man page Source code
exactTest Man page Source code
exactTestBetaApprox Man page Source code
exactTestByDeviance Man page Source code
exactTestBySmallP Man page Source code
exactTestDoubleTail Man page Source code
expandAsMatrix Man page Source code
fry.DGEList Man page Source code
getCounts Man page Source code
getDispersion Man page Source code
getDispersions Man page Source code
getOffset Man page Source code
getPriorN Man page Source code
getRecord Source code
gini Man page Source code
glmFit Man page Source code
glmFit.DGEList Man page Source code
glmFit.default Man page Source code
glmLRT Man page Source code
glmQLFTest Man page Source code
glmQLFit Man page Source code
glmQLFit.DGEList Man page Source code
glmQLFit.default Man page Source code
glmTreat Man page Source code
goana.DGEExact Man page
goana.DGELRT Man page Source code
gof Man page Source code
goodTuring Man page Source code
goodTuringPlot Man page Source code
goodTuringProportions Man page Source code
kegga.DGEExact Man page
kegga.DGELRT Man page Source code
locfitByCol Man page Source code
loessByCol Man page Source code
maPlot Man page Source code
makeCompressedMatrix Man page Source code
maximizeInterpolant Man page Source code
maximizeQuadratic Man page Source code
mglm Man page
mglmLevenberg Man page Source code
mglmOneGroup Man page Source code
mglmOneWay Man page Source code
movingAverageByCol Man page Source code
mroast.DGEList Man page Source code
nbinomDeviance Man page Source code
nbinomUnitDeviance Man page Source code
normalizeChIPtoInput Man page Source code
ntegratepnorm Source code
onAttach Source code
plotBCV Man page Source code
plotExonUsage Man page Source code
plotMD.DGEExact Man page Source code
plotMD.DGEGLM Man page Source code
plotMD.DGELRT Man page Source code
plotMD.DGEList Man page Source code
plotMDS.DGEList Man page Source code
plotMeanVar Man page Source code
plotQLDisp Man page Source code
plotSmear Man page Source code
plotSpliceDGE Man page Source code
predFC Man page Source code
predFC.DGEList Man page Source code
predFC.default Man page Source code
processAmplicons Man page Source code
psi.huber.matrix Source code
q2qnbinom Man page Source code
q2qpois Man page Source code
readDGE Man page Source code
residDF Source code
roast.DGEList Man page Source code
romer.DGEList Man page Source code
rpkm Man page Source code
rpkm.DGEList Man page Source code
rpkm.default Man page Source code
sAllZero Source code
sBelowPoissonBound Source code
scaleOffset Man page Source code
scaleOffset.DGEList Man page Source code
scaleOffset.default Man page Source code
show,DGEExact-method Man page
show,DGEGLM-method Man page
show,DGELRT-method Man page
show,TopTags-method Man page
spliceVariants Man page Source code
splitIntoGroups Man page Source code
splitIntoGroups.DGEList Man page Source code
splitIntoGroups.default Man page Source code
splitIntoGroupsPseudo Man page Source code
subsetMatrixWithoutCopying Source code
subsetting Man page
sumTechReps Man page Source code
sumTechReps.DGEList Man page Source code
sumTechReps.default Man page Source code
systematicSubset Man page Source code
thinCounts Man page Source code
topSpliceDGE Man page Source code
topTags Man page Source code
validDGEList Man page Man page Source code
weightedCondLogLikDerDelta Man page Source code
zscoreDGE Source code
zscoreNBinom Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/DGEList.R
R/S3methods.R
R/addPriorCount.R
R/adjustedProfileLik.R
R/aveLogCPM.R
R/binomTest.R
R/calcNormFactors.R
R/calcNormOffsets.R
R/classes.R
R/commonCondLogLikDerDelta.R
R/condLogLikDerDelta.R
R/condLogLikDerSize.R
R/cpm.R
R/cutWithMinN.R
R/decidetestsDGE.R
R/dglmStdResid.R
R/diffSpliceDGE.R
R/dispBinTrend.R
R/dispCoxReid.R
R/dispCoxReidInterpolateTagwise.R
R/dispCoxReidPowerTrend.R
R/dispCoxReidSplineTrend.R
R/dispDeviance.R
R/dispPearson.R
R/dropEmptyLevels.R
R/edgeRUsersGuide.R
R/equalizeLibSizes.R
R/estimateCommonDisp.R
R/estimateDisp.R
R/estimateGLMCommonDisp.R
R/estimateGLMRobustDisp.R
R/estimateGLMTagwiseDisp.R
R/estimateGLMTrendedDisp.R
R/estimateTagwiseDisp.R
R/estimateTrendedDisp.R
R/exactTest.R
R/exactTestBetaApprox.R
R/exactTestByDeviance.R
R/exactTestBySmallP.R
R/exactTestDoubleTail.R
R/expandAsMatrix.R
R/geneset-DGEList.R
R/getCounts.R
R/getDispersion.R
R/getOffset.R
R/getPriorN.R
R/gini.R
R/glmQLFTest.R
R/glmTreat.R
R/glmfit.R
R/goana.R
R/gof.R
R/goodTuring.R
R/kegga.R
R/locfitByCol.R
R/loessByCol.R
R/maPlot.R
R/makeCompressedMatrix.R
R/maximizeInterpolant.R
R/maximizeQuadratic.R
R/meanvar.R
R/mglmLevenberg.R
R/mglmOneGroup.R
R/mglmOneWay.R
R/movingAverageByCol.R
R/nbinomDeviance.R
R/normalizeChIPtoInput.R
R/plotBCV.R
R/plotMD.R
R/plotMDS.DGEList.R
R/plotSmear.R
R/predFC.R
R/processAmplicons.R
R/q2qnbinom.R
R/readDGE.R
R/residDF.R
R/rpkm.R
R/scaleOffset.R
R/spliceVariants.R
R/splitIntoGroups.R
R/splitIntoGroupsPseudo.R
R/subsetting.R
R/sumTechReps.R
R/systematicSubset.R
R/thinCounts.R
R/topTags.R
R/validDGEList.R
R/weightedCondLogLikDerDelta.R
R/zscoreNBinom.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/edgeR.Rnw
inst/doc/edgeR.pdf
inst/doc/edgeRUsersGuide.pdf
inst/doc/index.html
man
man/DGEExact-class.Rd
man/DGEGLM-class.Rd
man/DGELRT-class.Rd
man/DGEList-class.Rd
man/DGEList.Rd
man/WLEB.Rd
man/addPriorCount.Rd
man/adjustedProfileLik.Rd
man/asdataframe.Rd
man/asmatrix.Rd
man/aveLogCPM.Rd
man/binomTest.Rd
man/calcNormFactors.Rd
man/camera.DGEList.Rd
man/commonCondLogLikDerDelta.Rd
man/condLogLikDerSize.Rd
man/cpm.Rd
man/cutWithMinN.Rd
man/decidetestsDGE.Rd
man/dglmStdResid.Rd
man/diffSpliceDGE.Rd
man/dim.Rd
man/dimnames.Rd
man/dispBinTrend.Rd
man/dispCoxReid.Rd
man/dispCoxReidInterpolateTagwise.Rd
man/dispCoxReidSplineTrend.Rd
man/dropEmptyLevels.Rd
man/edgeR-package.Rd
man/edgeRUsersGuide.Rd
man/equalizeLibSizes.Rd
man/estimateCommonDisp.Rd
man/estimateDisp.Rd
man/estimateExonGenewisedisp.Rd
man/estimateGLMCommonDisp.Rd
man/estimateGLMRobustDisp.Rd
man/estimateGLMTagwiseDisp.Rd
man/estimateGLMTrendedDisp.Rd
man/estimateTagwiseDisp.Rd
man/estimateTrendedDisp.Rd
man/exactTest.Rd
man/expandAsMatrix.Rd
man/getCounts.Rd
man/getPriorN.Rd
man/gini.Rd
man/glmQLFTest.Rd
man/glmTreat.Rd
man/glmfit.Rd
man/goana.Rd
man/gof.Rd
man/goodTuring.Rd
man/loessByCol.Rd
man/maPlot.Rd
man/makeCompressedMatrix.Rd
man/maximizeInterpolant.Rd
man/maximizeQuadratic.Rd
man/meanvar.Rd
man/mglm.Rd
man/movingAverageByCol.Rd
man/nbinomDeviance.Rd
man/normalizeChIPtoInput.Rd
man/plotBCV.Rd
man/plotExonUsage.Rd
man/plotMD.Rd
man/plotMDS.DGEList.Rd
man/plotQLDisp.Rd
man/plotSmear.Rd
man/plotSpliceDGE.Rd
man/predFC.Rd
man/processAmplicons.Rd
man/q2qnbinom.Rd
man/readDGE.Rd
man/roast.DGEList.Rd
man/romer.DGEList.Rd
man/scaleOffset.Rd
man/spliceVariants.Rd
man/splitIntoGroups.Rd
man/subsetting.Rd
man/sumTechReps.Rd
man/systematicSubset.Rd
man/thinCounts.Rd
man/topSpliceDGE.Rd
man/topTags.Rd
man/validDGEList.Rd
man/weightedCondLogLikDerDelta.Rd
man/zscoreNBinom.Rd
src
src/Makevars
src/R_add_prior_count.cpp
src/R_add_repeat_matrices.cpp
src/R_ave_log_cpm.cpp
src/R_calculate_cpm.cpp
src/R_check_counts.cpp
src/R_check_poisson_bound.cpp
src/R_compute_apl.cpp
src/R_compute_nbdev.cpp
src/R_exact_test_by_deviance.cpp
src/R_get_one_way_fitted.cpp
src/R_initialize_levenberg.cpp
src/R_levenberg.cpp
src/R_loess_by_col.cpp
src/R_maximize_interpolant.cpp
src/R_one_group.cpp
src/R_process_hairpin_reads.c
src/R_simple_good_turing.cpp
src/add_prior.cpp
src/add_prior.h
src/adj_coxreid.cpp
src/fmm_spline.c
src/glm.h
src/glm_levenberg.cpp
src/glm_one_group.cpp
src/init.cpp
src/interpolator.cpp
src/interpolator.h
src/matvec_check.cpp
src/matvec_check.h
src/nbdev.cpp
src/utils.h
tests
tests/edgeR-Tests.R
tests/edgeR-Tests.Rout.save
vignettes
vignettes/edgeR.Rnw
edgeR documentation built on May 20, 2017, 9:21 p.m.

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