ChrEpi                  Sample MPRA data
MpraObject              MpraObject
analyzeComparative      Run a comparative analysis between conditions
analyzeQuantification   Perform quantitative analysis on the MPRA data.
                        This analysis aims to determine which sequences
                        have a regulatory function, when no condition
                        is being tested.
estimateDepthFactors    estimate library size correction factors
getAlpha                return the fitted value for the transcription
                        rate.
getDistrParam_DNA       Get model distribution parameters from an
                        MpraObject of a given candidate enhancer
getFits_DNA             Get DNA model-based estimates from an
                        MpraObject (the expected values based on the
                        model). These can be compared with the observed
                        counts to assess goodness of fit.
getFits_RNA             Get RNA model-based estimates from an
                        MpraObject (the expected values based on the
                        model). These can be compared with the observed
                        counts to assess goodness of fit.
getModelParameters_DNA
                        extract the DNA model parameters
setDepthFactors         Manually set library depth correction factors
setModel                Set the distributional model used. Default is
                        gamma.pois, and is recommended. Other supoprted
                        models are ln.nb in which the DNA follows a
                        log-normal distribution and the RNA follows a
                        negative binomial, and ln.ln in which both
                        follow log-normal distributions. To use
                        alternative distributional models, use this
                        function before fitting the model.
simulateMPRA            Simulate an MPRA dataset
testCoefficient         Calculate the significance of a factor in the
                        regression model
testEmpirical           test for significant activity (quantitative
                        analysis) using various empirical tests (see
                        details)
testLrt                 Calculate likelihood ratio test for the
                        specific nested model
