Digital gene expresion analysis based on the negative binomial distribution

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Documentation for package ‘DESeq’ version 1.2.1

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adjustScvForBias Adjust an SCV value for the bias arising when it is calculated from
conditions Accessor function for the conditions information in a CountDataSet
CountDataSet-class Class "CountDataSet" - a container for count data from HTS experiments
counts Accessor for the 'counts' slot of a CountDataSet object.
estimatePooledVarianceFunctionForMatrix Lower-level functions to estimate a raw variance function.
estimateSizeFactors Estimate the size factors for a CountDataSet
estimateSizeFactorsForMatrix Low-level function to estimate size factors with robust regression.
estimateVarianceFunctionForMatrix Lower-level functions to estimate a raw variance function.
estimateVarianceFunctions Estimate the variance functions for a CountDataSet.
getBaseMeansAndVariances Perform row-wise estimates of base-level means and variances for count
getRawScvDistanceMatrix Calculates a matrix of "distances" between samples
getRawScvForSamplePair for a pair of samples, calculate the average raw SCV between them, as a
getVarianceStabilizedData Perform a variance stabilising transformation (VST) on the count data
makeExampleCountDataSet make a simple example CountDataSet with random data
nbinomFitGLM Fit a generalized linear model (GLM) for each gene.
nbinomGLMsForMatrix Fit negative binomial GLMs to a count matrix.
nbinomGLMTest Perform chi-squared tests comparing two sets of GLM fits
nbinomTest Test for differences between the base means for two conditions
nbinomTestForMatrices Perform row-wise tests for differences between the base means of two
nbkd.sf GLM family for a negative binomial with known dispersion and log link
newCountDataSet Create a CountDataSet object
rawVarFunc Accessor for raw variance functions
rawVarFuncTable Accessor functions for the slot rawVarFuncTable of the class
rawVarFuncTable<- Accessor functions for the slot rawVarFuncTable of the class
residualsEcdfPlot Produce a diagnostic plot to check the fit of a raw variance function.
residualsEcdfPlotFromDiagnostics Produce a diagnostic plot to check the fit of a raw variance function.
scvPlot Produces a diagnostic plot with the variance estimates, given as
sizeFactors Accessor functions for the sizeFactors information in a CountDataSet
sizeFactors<- Accessor functions for the sizeFactors information in a CountDataSet
varAdjFactors Defunct function. Do not use.
varAdjFactors<- Defunct function. Do not use.
varianceFitDiagnostics Generate a data frame with diagnostic information on the fit of a base
varianceFitDiagnosticsForMatrix A lower-level function to get fit diagnostics