Empirical analysis of digital gene expression data in R


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Documentation for package ‘edgeR’ version 1.0.4

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alpha.approxeb Estimate the prior weight, alpha
approx.expected.info Approximate of expected information (Fisher information)
condLogLikDerDelta Conditional log-likelihood in terms of delta
condLogLikDerSize Conditional log-likelihood in terms of size
deDGE Compute moderated differential expression scores for digital gene expression (DGE) data
deDGEList-class differential expression of Digital Gene Expression data - class
DGEList Digital Gene Expression data - class
DGEList-class Digital Gene Expression data - class
EBList-class differential expression of Digital Gene Expression data - class
estimatePs Estimate expression proportions
exactTestNB An exact test for differences between two negative binomial groups
findMaxD2 Maximizes the negative binomial likelihood
getData Extract data table from DGEList object
interpolateHelper Quantile Adjustment interpolator
logLikDerP Log-likelihood for proportion
plotMA MA-like plot for deDGEList objects
plotMA,deDGEList-method MA-like plot for deDGEList objects
quantileAdjust Normalizes a dataset by using a quantile adjustment
readDGE Read a list of files containing DGE data
show,deDGEList-method differential expression of Digital Gene Expression data - class
show,DGEList-method Digital Gene Expression data - class
show,EBList-method differential expression of Digital Gene Expression data - class
tau2.0.objective Objective function for tau2
topTags Displays the top differentially expressed tags in a table