Empirical analysis of digital gene expression data in R


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Documentation for package ‘edgeR’ version 2.2.5

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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.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

-- 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
estimateCRDisp Estimate Negative Binomial Dispersion By Cox-Reid Adjusted Profile Likelihood (Obsolete)
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 Tagwise Dispersions for Negative Binomial GLMs
estimateGLMTagwiseDisp.default Estimate Tagwise Dispersions for Negative Binomial GLMs
estimateGLMTagwiseDisp.DGEList Estimate 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
estimateTagwiseDisp Maximizes the Negative Binomial Weighted Conditional Likelihood
exactTest An Exact Test for Differences between Two Negative Binomial Groups
exactTest.matrix An Exact Test for Differences between Two Negative Binomial Groups
expandAsMatrix expandAsMatrix

-- G --

getCounts Extract Table of Counts from DGEList Object
getDispersions Visualize the mean-variance relationship in DGE data using standardized residuals
getOffsets Extract Vector of Offsets from DGEList Object
glmFit 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 --

plotMDS.dge Multidimensional scaling plot of digital gene expression data
plotMeanVar Explore the mean-variance relationship for DGE data
plotSmear Plots log-Fold Change versus log-Concentration (or, M versus A) for Count Data
pooledVar Explore the mean-variance relationship for DGE 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
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, 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, DGEExact and DGELRT Objects
[.DGEList Subset DGEList, DGEExact and DGELRT Objects
[.DGELRT Subset DGEList, DGEExact and DGELRT Objects
[.TopTags Table of the Top Differentially Expressed Tags