adjustScvForBias | Adjust an SCV value for the bias arising when it is calculated from unbiased estimates of mean and variance. |
conditions | Accessor functions for the 'conditions' information in a CountDataSet object. |
conditions-method | Accessor functions for the 'conditions' information in a CountDataSet object. |
conditions<--method | Accessor functions for the 'conditions' information in a CountDataSet object. |
CountDataSet-class | Class "CountDataSet" - a container for count data from HTS experiments |
counts | Accessors for the 'counts' slot of a CountDataSet object. |
counts-method | Accessors for the 'counts' slot of a CountDataSet object. |
counts<--method | Accessors for the 'counts' slot of a CountDataSet object. |
dispTable | Accessor function for the dispTable information in a CountDataSet |
dispTable-method | Accessor function for the dispTable information in a CountDataSet |
estimateDispersions | Estimate and fit dispersions for a CountDataSet. |
estimateDispersions-method | Estimate and fit dispersions for a CountDataSet. |
estimateSizeFactors | Estimate the size factors for a CountDataSet |
estimateSizeFactors-method | Estimate the size factors for a CountDataSet |
estimateSizeFactorsForMatrix | Low-level function to estimate size factors with robust regression. |
estimateVarianceFunctions | REMOVED |
fitInfo | Accessor function for the fitInfo objects in a CountDataSet |
fitNbinomGLMs | Fit a generalized linear model (GLM) for each gene. |
fitNbinomGLMsForMatrix | Fit negative binomial GLMs to a count matrix. |
getBaseMeansAndVariances | Perform row-wise estimates of base-level means and variances for count data. |
getVarianceStabilizedData | Apply a variance stabilizing transformation (VST) to the count data |
makeExampleCountDataSet | make a simple example CountDataSet with random data |
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 count matrices. |
nbkd.sf | GLM family for a negative binomial with known dispersion and log link with size factors |
newCountDataSet | Create a CountDataSet object |
newCountDataSetFromHTSeqCount | Create a new CountDataSet from count files generated with htseq-count |
plotDispEsts | Plot dispersion estimates and fitted values |
plotMA | Makes a so-called "MA-plot" |
plotPCA | Sample PCA plot from variance-stabilized data |
residualsEcdfPlot | REMOVED |
scvPlot | REMOVED |
sizeFactors | Accessor functions for the 'sizeFactors' information in a CountDataSet object. |
sizeFactors-method | Accessor functions for the 'sizeFactors' information in a CountDataSet object. |
sizeFactors<--method | Accessor functions for the 'sizeFactors' information in a CountDataSet object. |
varianceFitDiagnostics | REMOVED |
varianceStabilizingTransformation | Apply a variance stabilizing transformation (VST) to the count data |