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 |