checkInputData          Generic function to check if the input data
                        fulfills all requirements for protein inference
                        with MIPGEM or quantification with SCAMPI.
checkInputData.scampi   Check if input object fulfills all requirements
                        in order to proceed with the protein
                        quantification step.
estimateModelParameters
                        Estimate the SCAMPI model paramteres alpha,
                        beta, mu and tau from the data
getCovU                 Compute covariance matrix of peptide abundances
iterateScampi           SCAMPI protein quantification function with
                        iterative outlier removal
leptoSRM                SRM quantification example data
leptoSRMedgespp         SRM quantification: edges informationu.
leptoSRMpeptides        SRM quantification: peptide example data
leptoSRMproteins        SRM quantification: protein example data
preprocessInputData     Generic function to preprocess the input data
                        for protein inference with MIPGEM or
                        quantification with SCAMPI to speed up further
                        computations.
preprocessInputData.scampi
                        Precompute all quantities which will be used
                        (repetitously) for further computations and do
                        not depend on the parameter values.
protiq-package          Protein (identification and) quantification
                        based on peptide evidence
quantifyPeptide         Compute expected value for the peptide
                        abundance.
quantifyProtein         Compute expected value and variance of a
                        protein abundance.
quantifyProteins        Compute the protein (and optionally the
                        peptide) abundance scores.
runScampi               SCAMPI protein quantification function
scampi-class            Class '"scampi"'
scampiVal-class         Class '"scampiVal"'
