StatModel-class         The StatModel class for msqrob
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,QFeatures-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.
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
pe                      Example data for 100 proteins
smallestUniqueGroups    Smallest unique protein groups
topFeatures             Toplist of DE proteins, peptides or features
