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 |