adjustScvForBias | Adjust an SCV value for the bias arising when it is calculated from unbiased estimates of mean and variance. |
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. |
estimateSizeFactors | Estimate the size factors for a CountDataSet |
estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust regression. |
estimateVarianceFunctionForMatrix | Lower-level function 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 data. |
getVarianceStabilizedData | Perform a variance stabilising transformation (VST) on the count data |
makeExampleCountDataSet | make a simple example CountDataSet with random data |
nbinomTest | Test for differences between the base means for two conditions |
nbinomTestForMatrices | Perform row-wise tests for differences between the base means of two count matrices. |
newCountDataSet | Create a CountDataSet object |
rawVarFunc | Accessor for raw variance functions |
rawVarFuncTable | Accessor function for the slot rawVarFuncTable of the class CountDataSet |
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 squared coefficients of variation (SCV) |
sizeFactors | Accessor functions for the sizeFactors information in a CountDataSet |
sizeFactors<- | Accessor functions for the sizeFactors information in a CountDataSet |
varianceFitDiagnostics | Generate a data frame with diagnostic information on the fit of a base variance function. |
varianceFitDiagnosticsForMatrix | A lower-level function to get fit diagnostics |