# Empirical analysis of digital gene expression data in R

## Documentation for package ‘edgeR’ version 2.4.6

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

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

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

## -- A --

adjustedProfileLik | Compute Cox-Reid Adjusted Profile Likelihood for Negative Binomial GLMs
approx.expected.info | Approximate Expected Information (Fisher Information)
as.data.frame.TopTags | Turn a TopTags Object into a Dataframe
as.matrix.DGEList | Turn a DGEList Object into a Matrix

## -- B --

betaApproxNBTest | An Approximate Exact Test for Differences between Two Negative Binomial Groups
binCMLDispersion | Estimate Common Dispersion for Negative Binomial GLMs in Bins of Genes Sorted by Overall Abundance
binGLMDispersion | Estimate Common Dispersion for Negative Binomial GLMs in Bins of Genes Sorted by Overall Abundance
binMeanVar | Explore the mean-variance relationship for DGE data
binomTest | Exact Binomial Tests for Comparing Two Digital Libraries

## -- C --

calcNormFactors | Calculates Normalization Factors for a Matrix of Count Data
commonCondLogLikDerDelta | Conditional Log-Likelihoods in Terms of Delta
condLogLikDerDelta | Conditional Log-Likelihood in Terms of Delta
condLogLikDerSize | Log-Likelihood of the Common Dispersion for a Single Equalized Group
cpm | Calculate Counts per Million from DGEList or Matrix Object
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
deviances.function | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors
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
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.DGEList | Retrieve the Dimension Names of a DGEList Object
dimnames<-.DGEList | Retrieve the Dimension Names of a DGEList Object
dispBinTrend | Estimate Dispersions with an Abundance-Dependent Trend for Negative Binomial 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
equalizeLibSizes | Quantile Adjustment to Equalize Library Sizes for a Fixed Value of the Dispersion Parameter
estimateCommonDisp | Estimates the Negative Binomial Common Dispersion by Maximizing the Negative Binomial Conditional Common Likelihood
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
estimateGLMTagwiseDisp | Estimate Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs
estimateGLMTagwiseDisp.default | Estimate Empirical Bayes Tagwise Dispersions for Negative Binomial GLMs
estimateGLMTagwiseDisp.DGEList | Estimate 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
estimatePs | Estimate Expression Levels
estimateSmoothing | Estimate the Prior Weight for Tagwise Dispersions
estimateTagwiseDisp | Estimate Empirical Bayes Tagwise 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 | Fit negative binomial generalized linear model for each transcript
glmFit.default | Fit negative binomial generalized linear model for each transcript
glmFit.DGEList | Fit negative binomial generalized linear model for each transcript
glmLRT | Fit negative binomial generalized linear model for each transcript
gof | Goodness of Fit Tests for Multiple GLM Fits
goodTuring | 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
logLikDerP | Log-Likelihood for Proportion

## -- 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.
mglm | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors
mglmLevenberg | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors
mglmLS | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors
mglmOneGroup | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors
mglmOneWay | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors
mglmSimple | Fit Negative Binomial Generalized Linear Model to Multiple Response Vectors
movingAverageByCol | Moving Average Smoother of Matrix Columns

## -- N --

NC1 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.
NC2 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.

## -- P --

plotExonUsage | Create a Plot of Exon Usage from Exon-Level Count Data
plotMDS.DGEList | Multidimensional scaling plot of digital gene expression profiles
plotMeanVar | Explore the mean-variance relationship for DGE data
plotSmear | Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data

## -- 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

## -- 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
systematicSubset | Take a systematic subset of indices.

## -- T --

thinCounts | Binomial Thinning of Counts
topTags | Table of the Top Differentially Expressed Tags
TopTags-class | Table of the Top Differentially Expressed Tags
Tu102 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.
Tu98 | Raw Data for Several SAGE Libraries from the Zhang 1997 Science Paper.

## -- W --

weightedComLik | Weighted Common Log-Likelihood
weightedComLikMA | Weighted Common Log-Likelihood
weightedCondLogLikDerDelta | Weighted Conditional Log-Likelihood in Terms of Delta

## -- 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 | Table of the Top Differentially Expressed Tags