Empirical analysis of digital gene expression data in R

Documentation for package ‘edgeR’ version 3.12.1

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

Empirical analysis of digital gene expression data in R

-- A --

adjustedProfileLik	Adjusted Profile Likelihood for the Negative Binomial Dispersion Parameter
as.data.frame.TopTags	Turn a TopTags Object into a Dataframe
as.matrix.DGEList	Turn a DGEList Object into 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

-- B --

binMeanVar	Explore the mean-variance relationship for DGE data
binomTest	Exact Binomial Tests for Comparing Two Digital Libraries

-- C --

calcNormFactors	Calculate Normalization Factors to Align Columns of a Count Matrix
calcNormFactors.default	Calculate Normalization Factors to Align Columns of a Count Matrix
calcNormFactors.DGEList	Calculate Normalization Factors to Align Columns of a Count Matrix
calcNormOffsetsforChIP	Normalize ChIP-Seq Read Counts to Input and Test for Enrichment
camera.DGEList	Competitive Gene Set Test for Digital Gene Expression Data Accounting for Inter-gene Correlation
commonCondLogLikDerDelta	Conditional Log-Likelihoods in Terms of Delta
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.DGEList	Counts per Million or Reads per Kilobase per Million
cutWithMinN	Cut numeric vector into non-empty intervals

-- D --

decideTestsDGE	Multiple Testing Across Genes and Contrasts
designAsFactor	Fit Negative Binomial Generalized Linear Model 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	DGEList Constructor
DGEList-class	Digital Gene Expression data - class
DGELRT-class	Digital Gene Expression Likelihood Ratio Test data and results - class
dglmStdResid	Visualize the mean-variance relationship in DGE data using standardized residuals
diffSpliceDGE	Test for Differential Exon Usage
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
estimateCommonDisp	Estimate Common Negative Binomial Dispersion by Conditional Maximum Likelihood
estimateDisp	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
estimateTrendedDisp	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

-- G --

getCounts	Extract Specified Component of a DGEList Object
getDispersion	Extract Specified Component of a DGEList Object
getDispersions	Visualize the mean-variance relationship in DGE data using standardized residuals
getOffset	Extract Specified Component of a DGEList Object
getPriorN	Get a Recommended Value for Prior N from DGEList Object
glmFit	Genewise Negative Binomial Generalized Linear Models
glmFit.default	Genewise Negative Binomial Generalized Linear Models
glmFit.DGEList	Genewise Negative Binomial Generalized Linear Models
glmLRT	Genewise Negative Binomial Generalized Linear Models
glmQLFit	Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests
glmQLFit.default	Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests
glmQLFit.DGEList	Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood Tests
glmQLFTest	Genewise Negative Binomial Generalized Linear Models with Quasi-likelihood 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

-- 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.DGEExact	Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
length.DGEGLM	Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
length.DGEList	Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
length.DGELRT	Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
length.TopTags	Retrieve the Dimensions of a DGEList, DGEExact, DGEGLM, DGELRT or TopTags Object
locfitByCol	Locally Weighted Mean By Column
loessByCol	Locally Weighted Mean By Column

-- M --

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 Model to Multiple Response Vectors: Low Level Functions
mglmLevenberg	Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions
mglmOneGroup	Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions
mglmOneWay	Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors: Low Level Functions
movingAverageByCol	Moving Average Smoother of Matrix Columns
mroast.DGEList	Rotation Gene Set Tests for Digital Gene Expression Data

-- N --

nbinomDeviance	Negative Binomial Deviance
nbinomUnitDeviance	Negative Binomial Deviance
normalizeChIPtoInput	Normalize ChIP-Seq Read Counts to Input and Test for Enrichment

-- 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
plotMDS.DGEList	Multidimensional scaling plot of distances between digital gene expression profiles
plotMeanVar	Explore the mean-variance relationship for DGE data
plotQLDisp	Plot the quasi-likelihood dispersion
plotSmear	Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data
plotSpliceDGE	Differential splicing plot
predFC	Predictive log-fold changes
predFC.default	Predictive log-fold changes
predFC.DGEList	Predictive log-fold changes
processAmplicons	Process raw data 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 --

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
rpkm	Counts per Million or Reads per Kilobase per Million
rpkm.default	Counts per Million or Reads per Kilobase per Million
rpkm.DGEList	Counts per Million or Reads per Kilobase per Million

-- S --

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 Tags
spliceVariants	Identify Genes with Splice Variants
splitIntoGroups	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
systematicSubset	Take a systematic subset of indices.

-- T --

thinCounts	Binomial or Multinomial Thinning of Counts
topSpliceDGE	Top table of differentially spliced genes or exons
topTags	Table of the Top Differentially Expressed Tags
TopTags-class	Table of the Top Differentially Expressed Tags
treatDGE	Test for Differential Expression Relative to a Threshold

-- V --

validDGEList

Check for Valid DGEList object

-- W --

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

-- Z --

zscoreNBinom

Z-score Equivalents of Negative Binomial Deviate

-- misc --

[.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