Empirical analysis of digital gene expression data in R

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Documentation for package ‘edgeR’ version 3.8.6

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edgeR-package 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<-.DGEGLM Retrieve the Dimension Names of a DGE Object
dimnames<-.DGEList 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 Tagwise 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

-- 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 Quasi-likelihood methods with empirical Bayes shrinkage
glmQLFTest Quasi-likelihood methods with empirical Bayes shrinkage
goana.DGEExact Gene Ontology Analysis of Differentially Expressed Genes
goana.DGELRT Gene Ontology 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

-- 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
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 Plot exons on differentially spliced gene
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 DGE Data
roast.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 Testing 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