MVgen                   Amputation of a dataset
check.conditions        Check if the design is valid
check.design            Check if the design is valid
datasim                 A single simulated dataset
eBayes.mod              MI-aware Modifed eBayes Function
formatLimmaResult       Format a Result from Limma
hid.ebayes              MI-aware Modifed eBayes Function
limmaCompleteTest.mod   Computes a hierarchical differential analysis
make.contrast           Builds the contrast matrix
make.design             Builds the design matrix
make.design.1           Builds the design matrix for designs of level 1
make.design.2           Builds the design matrix for designs of level 2
make.design.3           Builds the design matrix for designs of level 3
meanImp_emmeans         Multiple Imputation Estimate
mi4limma                Differential analysis after multiple imputation
mm_peptides             mm_peptides - peptide-level intensities for
                        mouse
multi.impute            Multiple imputation of quantitative proteomics
                        datasets
norm.200.m100.sd1.vs.m200.sd1.list
                        A list of simulated datasets.
proj_matrix             Variance-Covariance Matrix Projection
protdatasim             Data simulation function
qData                   Extract of the abundances of Exp1_R25_pept
                        dataset
rubin1.all              First Rubin rule (all peptides)
rubin1.one              First Rubin rule (a given peptide)
rubin2.all              Computes the 2nd Rubin's rule (all peptides)
rubin2bt.all            2nd Rubin's rule Between-Imputation component
                        (all peptides)
rubin2bt.one            2nd Rubin's rule Between-Imputation Component
                        (a given peptide)
rubin2wt.all            2nd Rubin's rule Within-Variance Component (all
                        peptides)
rubin2wt.one            2nd Rubin's rule Within-Variance Component (a
                        given peptide)
sTab                    Experimental design for the Exp1_R25_pept
                        dataset
test.design             Check if xxxxxx
within_variance_comp_emmeans
                        Multiple Imputation Within Variance Component
