.computeNfLogMedian     Helper function to calculate sample-specific
                        normalization factors on the log2 scale using
                        conventional median normalisation
.computeNfLogMedianOfRatios
                        Helper function to calculate sample-specific
                        normalization factors
createPairwiseContrasts
                        Construct all contrasts for all pairwise
                        comparisons between all levels of a factor
getContrast,StatModel-method
                        Methods for StatModel class
getModel,StatModel-method
                        Accessor functions for StatModel class
hypothesisTest,SummarizedExperiment-method
                        Parameter estimates, standard errors and
                        statistical inference on differential
                        expression analysis
makeContrast            Make contrast matrix
msqrob,SummarizedExperiment-method
                        Methods to fit msqrob models with ridge
                        regression and/or random effects using lme4
msqrobAggregate,SummarizedExperiment-method
                        Method to fit msqrob models with robust
                        regression and/or ridge regression and/or
                        random effects It models multiple features
                        simultaneously, e.g. multiple peptides from the
                        same protein.
msqrobCollect           Function to collect the inference tables
                        generated by the msqrob2 statistical inference
                        workflow.
msqrobGlm               Function to fit msqrob models to peptide counts
                        using glm
msqrobHurdle,SummarizedExperiment-method
                        Function to fit msqrob hurdle models
msqrobLm                Function to fit msqrob models using lm and rlm
msqrobLmer              Function to fit msqrob models with ridge
                        regression and/or random effects using lme4
msqrobQB,SummarizedExperiment-method
                        Function to fit msqrob models to peptide counts
                        using glm
nfLogMedian,matrix-method
                        Methods to computes sample-specific
                        normalization factors on the log scale using
                        conventional median summarisation.
nfLogMedianOfRatios,matrix-method
                        Methods to calculate log-scale normalization
                        factors using the median-of-ratios method
pe                      Example data for 100 proteins
plotVolcano             Volcano plot
smallestUniqueGroups    Smallest unique protein groups
StatModel-class         The StatModel class for msqrob
topFeatures             Toplist of DE proteins, peptides or features
