Empirical Analysis of Digital Gene Expression Data in R

Documentation for package ‘edgeR’ version 4.4.2

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

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 Salmon, kallisto or RSEM Transcript Output
catchRSEM	Process Salmon, kallisto or RSEM Transcript Output
catchSalmon	Process Salmon, kallisto 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.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
DGELRT-class	Digital Gene Expression Likelihood Ratio Test data and results - class
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 Specified Component of a DGEList Object
getDispersion	Extract Specified Component 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 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
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.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 --

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
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

-- 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