R: Empirical Analysis of Digital Gene Expression Data in R

# Empirical Analysis of Digital Gene Expression Data in R

## Documentation for package ‘edgeR’ version 4.11.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G H K L M N O P Q R S T V W Z misc

edgeR-package | Empirical analysis of digital gene expression data in R

## -- A --

addPriorCount | Add a prior count
adjustedProfileLik | Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter
as.data.frame.DGEExact | Collapse TopTags or Other edgeR Object to a Data Frame
as.data.frame.DGEGLM | Collapse TopTags or Other edgeR Object to a Data Frame
as.data.frame.DGEList | Collapse TopTags or Other edgeR Object to a Data Frame
as.data.frame.DGELRT | Collapse TopTags or Other edgeR Object to a Data Frame
as.data.frame.TopTags | Collapse TopTags or Other edgeR Object to a Data Frame
as.matrix.CompressedMatrix | Make a CompressedMatrix
as.matrix.DGEGLM | Collapse a DGEList or DGEGLM Object to a Matrix
as.matrix.DGEList | Collapse a DGEList or DGEGLM Object to a Matrix
aveLogCPM | Average Log Counts Per Million
aveLogCPM.default | Average Log Counts Per Million
aveLogCPM.DGEGLM | Average Log Counts Per Million
aveLogCPM.DGEList | Average Log Counts Per Million
aveLogCPM.SummarizedExperiment | Average Log Counts Per Million

## -- B --

binMeanVar | Explore the Mean-Variance Relationship for DGE Data
binomTest | Exact Binomial Tests for Comparing Two Digital Libraries

## -- C --

calcNormFactors | Normalize Library Sizes
calcNormFactors.default | Normalize Library Sizes
calcNormFactors.DGEList | Normalize Library Sizes
calcNormFactors.SummarizedExperiment | Normalize Library Sizes
calcNormOffsetsforChIP | Normalize ChIP-Seq Read Counts to Input and Test for Enrichment
camera.DGEGLM | Competitive Gene Set Tests for Digital Gene Expression Data
camera.DGEList | Competitive Gene Set Tests for Digital Gene Expression Data
cameraPR.DGELRT | Competitive Gene Set Tests for Digital Gene Expression Data
catchKallisto | Process kallisto, Salmon, Oarfish, or RSEM Transcript Output
catchOarfish | Process kallisto, Salmon, Oarfish, or RSEM Transcript Output
catchRSEM | Process kallisto, Salmon, Oarfish, or RSEM Transcript Output
catchSalmon | Process kallisto, Salmon, Oarfish, or RSEM Transcript Output
cbind | Combine DGEList Objects
cbind.CompressedMatrix | Make a CompressedMatrix
cbind.DGEList | Combine DGEList Objects
commonCondLogLikDerDelta | Conditional Log-Likelihoods in Terms of Delta
CompressedMatrix | Make a CompressedMatrix
CompressedMatrix-class | Make a CompressedMatrix
condLogLikDerDelta | Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries
condLogLikDerSize | Conditional Log-Likelihood of the Dispersion for a Single Group of Replicate Libraries
cpm | Counts per Million or Reads per Kilobase per Million
cpm.default | Counts per Million or Reads per Kilobase per Million
cpm.DGEGLM | Counts per Million or Reads per Kilobase per Million
cpm.DGEList | Counts per Million or Reads per Kilobase per Million
cpm.DGELRT | Counts per Million or Reads per Kilobase per Million
cpm.MArrayLM | Counts per Million or Reads per Kilobase per Million
cpm.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million
cpmByGroup | Counts per Million or Reads per Kilobase per Million
cpmByGroup.default | Counts per Million or Reads per Kilobase per Million
cpmByGroup.DGEList | Counts per Million or Reads per Kilobase per Million
cpmByGroup.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million
cutWithMinN | Cut Numeric Vector Into Non-empty Intervals

## -- D --

decideTests.DGEExact | Multiple Testing Across Genes and Contrasts
decideTests.DGELRT | Multiple Testing Across Genes and Contrasts
designAsFactor | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions
DGEExact-class | differential expression of Digital Gene Expression data - class
DGEGLM-class | Digital Gene Expression Generalized Linear Model results - class
DGEList | Create a DGEList object
DGEList-class | Digital Gene Expression data - class
DGEList.data.frame | Create a DGEList object
DGEList.default | Create a DGEList object
DGEListFromTximeta | Create a DGEList Object From tximport or tximeta Output
DGEListFromTximport | Create a DGEList Object From tximport or tximeta Output
DGELRT-class | Digital Gene Expression Likelihood Ratio Test data and results - class
diffSplice.DGEGLM | Differential Transcript or Exon Usage
diffSpliceDGE | Test for Differential Exon Usage
dim.CompressedMatrix | Make a CompressedMatrix
dim.DGEExact | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
dim.DGEGLM | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
dim.DGEList | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
dim.DGELRT | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
dim.TopTags | Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
dimnames.DGEExact | Retrieve the Dimension Names of a DGE Object
dimnames.DGEGLM | Retrieve the Dimension Names of a DGE Object
dimnames.DGEList | Retrieve the Dimension Names of a DGE Object
dimnames.DGELRT | Retrieve the Dimension Names of a DGE Object
dimnames.TopTags | Retrieve the Dimension Names of a DGE Object
dimnames<-.DGEExact | Retrieve the Dimension Names of a DGE Object
dimnames<-.DGEGLM | Retrieve the Dimension Names of a DGE Object
dimnames<-.DGEList | Retrieve the Dimension Names of a DGE Object
dimnames<-.DGELRT | 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
dispCoxReidPowerTrend | Estimate Dispersion Trend for Negative Binomial GLMs
dispCoxReidSplineTrend | Estimate Dispersion Trend for Negative Binomial GLMs
dispDeviance | Estimate Common Dispersion for Negative Binomial GLMs
dispPearson | Estimate Common Dispersion for Negative Binomial GLMs
dropEmptyLevels | Drop Levels of a Factor that Never Occur

## -- E --

edgeR | Empirical analysis of digital gene expression data in R
edgeRUsersGuide | View edgeR User's Guide
equalizeLibSizes | Equalize Library Sizes by Quantile-to-Quantile Normalization
equalizeLibSizes.default | Equalize Library Sizes by Quantile-to-Quantile Normalization
equalizeLibSizes.DGEList | Equalize Library Sizes by Quantile-to-Quantile Normalization
estimateCommonDisp | Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood
estimateCommonDisp.default | Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood
estimateCommonDisp.DGEList | Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood
estimateDisp | Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes
estimateDisp.default | Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes
estimateDisp.DGEList | Estimate Common, Trended and Tagwise Negative Binomial dispersions by weighted likelihood empirical Bayes
estimateDisp.SummarizedExperiment | 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
estimateGLMCommonDisp.default | Estimate Common Dispersion for Negative Binomial GLMs
estimateGLMCommonDisp.DGEList | 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
estimateGLMTagwiseDisp.default | Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs
estimateGLMTagwiseDisp.DGEList | Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs
estimateGLMTrendedDisp | Estimate Trended Dispersion for Negative Binomial GLMs
estimateGLMTrendedDisp.default | Estimate Trended Dispersion for Negative Binomial GLMs
estimateGLMTrendedDisp.DGEList | Estimate Trended Dispersion for Negative Binomial GLMs
estimateTagwiseDisp | Estimate Empirical Bayes Tagwise Dispersion Values
estimateTagwiseDisp.default | Estimate Empirical Bayes Tagwise Dispersion Values
estimateTagwiseDisp.DGEList | Estimate Empirical Bayes Tagwise Dispersion Values
estimateTrendedDisp | Estimate Empirical Bayes Trended Dispersion Values
estimateTrendedDisp.default | Estimate Empirical Bayes Trended Dispersion Values
estimateTrendedDisp.DGEList | Estimate Empirical Bayes Trended Dispersion Values
exactTest | Exact Tests for Differences between Two Groups of Negative-Binomial Counts
exactTestBetaApprox | Exact Tests for Differences between Two Groups of Negative-Binomial Counts
exactTestByDeviance | Exact Tests for Differences between Two Groups of Negative-Binomial Counts
exactTestBySmallP | Exact Tests for Differences between Two Groups of Negative-Binomial Counts
exactTestDoubleTail | Exact Tests for Differences between Two Groups of Negative-Binomial Counts
expandAsMatrix | expandAsMatrix

## -- F --

featureCounts2DGEList | Convert featureCounts object to a DGEList
filterByExpr | Filter Genes By Expression Level
filterByExpr.default | Filter Genes By Expression Level
filterByExpr.DGEList | Filter Genes By Expression Level
filterByExpr.SummarizedExperiment | Filter Genes By Expression Level
fry.DGEGLM | Self-contained Gene Set Tests for Digital Gene Expression Data
fry.DGEList | Self-contained Gene Set Tests for Digital Gene Expression Data

## -- G --

getCounts | Extract Components of a DGEList Object
getDispersion | Extract Components of a DGEList Object
getNormLibSizes | Effective Library Sizes
getNormLibSizes.default | Effective Library Sizes
getNormLibSizes.DGEGLM | Effective Library Sizes
getNormLibSizes.DGEList | Effective Library Sizes
getNormLibSizes.DGELRT | Effective Library Sizes
getOffset | Extract Components 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
glmFit.default | Genewise Negative Binomial Generalized Linear Models
glmFit.DGEList | Genewise Negative Binomial Generalized Linear Models
glmFit.SummarizedExperiment | Genewise Negative Binomial Generalized Linear Models
glmLRT | Genewise Likelihood Ratio Tests
glmQLFit | Genewise Negative Binomial Generalized Linear Models with Quasi-Dispersion Estimation
glmQLFit.default | Genewise Negative Binomial Generalized Linear Models with Quasi-Dispersion Estimation
glmQLFit.DGEList | Genewise Negative Binomial Generalized Linear Models with Quasi-Dispersion Estimation
glmQLFit.SummarizedExperiment | Genewise Negative Binomial Generalized Linear Models with Quasi-Dispersion Estimation
glmQLFTest | Quasi-Likelihood F-Tests
glmTreat | Test for Differential Expression Relative to a Threshold
goana.DGEExact | Gene Ontology or KEGG Analysis of Differentially Expressed Genes
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
goodTuringPlot | Good-Turing Frequency Estimation
goodTuringProportions | Good-Turing Frequency Estimation

## -- H --

head.DGEExact | Return the First to Last Part of a Data Object
head.DGEGLM | Return the First to Last Part of a Data Object
head.DGEList | Return the First to Last Part of a Data Object
head.DGELRT | Return the First to Last Part of a Data Object
head.TopTags | Return the First to Last Part of a Data Object

## -- K --

kegga.DGEExact | Gene Ontology or KEGG Analysis of Differentially Expressed Genes
kegga.DGELRT | Gene Ontology or KEGG Analysis of Differentially Expressed Genes

## -- L --

length.CompressedMatrix | Make a CompressedMatrix
locfitByCol | Locally Weighted Mean By Column
loessByCol | Locally Weighted Mean By Column

## -- M --

makeCompressedMatrix | Make a CompressedMatrix
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 Models to Multiple Response Vectors: Low Level Functions
mglmLevenberg | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions
mglmOneGroup | Fit Negative Binomial Generalized Linear Models to Multiple Response Vectors: Low Level Functions
mglmOneWay | 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
mroast.DGEGLM | Self-contained Gene Set Tests for Digital Gene Expression Data
mroast.DGEList | Self-contained Gene Set Tests for Digital Gene Expression Data

## -- N --

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
normalizeBetweenArrays.DGEList | Apply Microarray Normalization to DGEList
normalizeChIPtoInput | Normalize ChIP-Seq Read Counts to Input and Test for Enrichment
normLibSizes | Normalize Library Sizes
normLibSizes.default | Normalize Library Sizes
normLibSizes.DGEList | Normalize Library Sizes
normLibSizes.SummarizedExperiment | Normalize Library Sizes

## -- O --

Ops.CompressedMatrix | Make a CompressedMatrix

## -- P --

plotBCV | Plot Biological Coefficient of Variation
plotExonUsage | Create a Plot of Exon Usage from Exon-Level Count Data
plotMD.DGEExact | Mean-Difference Plot of Count Data
plotMD.DGEGLM | Mean-Difference Plot of Count Data
plotMD.DGEList | Mean-Difference Plot of Count Data
plotMD.DGELRT | Mean-Difference Plot of Count Data
plotMD.SummarizedExperiment | Mean-Difference Plot of Count Data
plotMDS.DGEList | Multidimensional scaling plot of distances between digital gene expression profiles
plotMDS.SummarizedExperiment | Multidimensional scaling plot of distances between digital gene expression profiles
plotMeanVar | Explore the Mean-Variance Relationship for DGE Data
plotMeanVar2 | Plot Mean-Variance Relationship in DGE Data Using Standardized Residuals
plotQLDisp | Plot the quasi-dispersion
plotSmear | Smear plot
plotSpliceDGE | Differential splicing plot
predFC | Predictive log-fold changes
predFC.default | Predictive log-fold changes
predFC.DGEList | Predictive log-fold changes
predFC.SummarizedExperiment | Predictive log-fold changes
processAmplicons | Process FASTQ files from pooled genetic sequencing screens

## -- Q --

q2qnbinom | Quantile to Quantile Mapping between Negative-Binomial Distributions
q2qpois | Quantile to Quantile Mapping between Negative-Binomial Distributions

## -- R --

rbind.CompressedMatrix | Make a CompressedMatrix
rbind.DGEList | Combine DGEList Objects
read10X | Read 10X Genomics Files
readBismark2DGE | Read Bismark Coverage Files
readDGE | Read and Merge a Set of Files Containing Count Data
roast.DGEGLM | Self-contained Gene Set Tests for Digital Gene Expression Data
roast.DGEList | Self-contained Gene Set Tests for Digital Gene Expression Data
romer.DGEGLM | Rotation Gene Set Enrichment for Digital Gene Expression Data
romer.DGEList | Rotation Gene Set Enrichment for Digital Gene Expression Data
rowsum.DGEList | Sum Over Groups of Genes
rowsum.SummarizedExperiment | Sum Over Groups of Genes
rpkm | Counts per Million or Reads per Kilobase per Million
rpkm.default | Counts per Million or Reads per Kilobase per Million
rpkm.DGEGLM | Counts per Million or Reads per Kilobase per Million
rpkm.DGEList | Counts per Million or Reads per Kilobase per Million
rpkm.DGELRT | Counts per Million or Reads per Kilobase per Million
rpkm.MArrayLM | Counts per Million or Reads per Kilobase per Million
rpkm.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million
rpkmByGroup | Counts per Million or Reads per Kilobase per Million
rpkmByGroup.default | Counts per Million or Reads per Kilobase per Million
rpkmByGroup.DGEList | Counts per Million or Reads per Kilobase per Million
rpkmByGroup.SummarizedExperiment | Counts per Million or Reads per Kilobase per Million

## -- S --

sampleWeights | Empirical Sample Quality Weights
scaleOffset | Scale offsets
scaleOffset.default | Scale offsets
scaleOffset.DGEList | Scale offsets
SE2DGEList | SummarizedExperiment to DGEList
Seurat2PB | Seurat or SeuratObject class object to pseudo-bulk DGEList
show-method | differential expression of Digital Gene Expression data - class
show-method | Digital Gene Expression Generalized Linear Model results - class
show-method | Digital Gene Expression Likelihood Ratio Test data and results - class
show-method | Table of the Top Differentially Expressed Genes/Tags
spliceVariants | Identify Genes with Splice Variants (Classic Pipeline)
splitIntoGroups | Split the Counts or Pseudocounts from a DGEList Object According To Group
splitIntoGroups.default | Split the Counts or Pseudocounts from a DGEList Object According To Group
splitIntoGroups.DGEList | Split the Counts or Pseudocounts from a DGEList Object According To Group
splitIntoGroupsPseudo | 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
sumTechReps.default | Sum Over Replicate Samples
sumTechReps.DGEList | Sum Over Replicate Samples
sumTechReps.SummarizedExperiment | Sum Over Replicate Samples
systematicSubset | Take a systematic subset of indices.

## -- T --

tail.DGEExact | Return the First to Last Part of a Data Object
tail.DGEGLM | Return the First to Last Part of a Data Object
tail.DGEList | Return the First to Last Part of a Data Object
tail.DGELRT | Return the First to Last Part of a Data Object
tail.TopTags | Return the First to Last Part of a Data Object
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
TopTags-class | Table of the Top Differentially Expressed Genes/Tags
tpm | Transcripts per Million
tpmProp | TPM Proportion By Transcript For Each Gene

## -- V --

validDGEList | Check for Valid DGEList object
voomLmFit | Apply voom-lmFit Pipeline While Accounting for Loss of Residual DF Due to Exact Zeros

## -- W --

weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta
WLEB | Weighted Likelihood Empirical Bayes

## -- Z --

zscoreNBinom | Z-score Equivalents of Negative Binomial Deviate

## -- misc --

[.CompressedMatrix | Make a CompressedMatrix
[.DGEExact | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
[.DGEGLM | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
[.DGEList | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
[.DGELRT | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
[.TopTags | Subset DGEList, DGEGLM, DGEExact and DGELRT Objects
[<-.CompressedMatrix | Make a CompressedMatrix