Empirical analysis of digital gene expression data in R

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Documentation for package ‘edgeR’ version 2.0.5

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edgeR-package Empirical analysis of digital gene expression data in R
adjustedProfileLik Estimate the dispersion parameter for a negative binomial model using Cox-Reid approximate conditional inference
approx.expected.info Approximate Expected Information (Fisher Information)
betaApproxNBTest An Approximate Exact Test for Differences between Two Negative Binomial Groups
binMeanVar Explore the mean-variance relationship for DGE data
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
decideTestsDGE Multiple Testing Across Genes and Contrasts
deviances.function Fit a 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
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 the dispersion parameter for a negative binomial model using Cox-Reid approximate conditional inference
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
getCounts Extract Table of Counts from DGEList Object
getDispersions Visualize the mean-variance relationship in DGE data using standardized residuals
glmFit Fit negative binomial generalized linear model for each transcript
glmLRT Fit negative binomial generalized linear model for each transcript
goodTuring Good-Turing Frequency Estimation
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
maPlot Plots Log-Fold Change versus Log-Concentration (or, M versus A) for Count Data
mglm Fit a negative binomial generalized linear model to multiple response vectors
mglmLS Fit a negative binomial generalized linear model to multiple response vectors
mglmOneGroup Fit a negative binomial generalized linear model to multiple response vectors
mglmSimple Fit a negative binomial generalized linear model to multiple response vectors
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.
plotMDS.dge Multidimensional scaling plot of SAGE 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
q2qnbinom Quantile to Quantile Mapping between Negative-Binomial Distributions
q2qpois Quantile to Quantile Mapping between Negative-Binomial Distributions
readDGE Read and Merge a Set of Files Containing DGE Data
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 and DGEExact Objects
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.
weightedComLik Weighted Common Log-Likelihood
weightedCondLogLikDerDelta Weighted Conditional Log-Likelihood in Terms of Delta
[.DGEExact Subset DGEList and DGEExact Objects
[.DGEList Subset DGEList and DGEExact Objects
[.TopTags Table of the Top Differentially Expressed Tags