Ftest.Ttest             A function to perform the paired t test for
                        each protein, and the Hotelling T test for the
                        group that the protein is assigned.
Ttest                   The function to calculate the p values for each
                        protein in the optim.two.stage.single function
calculate.cost          Function to calculate the total cost of the
                        multi-stage design
calculate.n3            A function to calculate the stage III sample
                        size based on the current design parameters
do.one.experiment       Simulation function for calculate the expected
                        number of detectable proteins from the three
                        stage proteomic study using group information
do.one.experiment.t     Simulation function for calculating the
                        expected number of detectable proteins from the
                        three stage proteomic study
genseq.appr             A sub function to generate the sub solution
                        space
genseq.group            A sub function to generate the sub solution
                        space
genseq.single           A sub function to generate the sub solution
                        space
optim.two.stage.appr    Optimize numbers of discoveries by using an
                        approximated analytical objective function in a
                        multi-stage clinical proteomic study that
                        utilizes biological group information
optim.two.stage.group   Optimization of the design parameters in the
                        discovery , verification and validation stage
                        from a multi-stage clinical proteomic study
                        using biological grouping information
optim.two.stage.single
                        Optimization of the number of discoveries from
                        a multistage clinical proteomic study
ots.env                 assign the current working environment
power                   The power function used in the
                        optim.two.stage.single function
power.appr              The power function used in the
                        optim.two.stage.appr function
power.group.cost        Derive the averaged estimated costs of stage II
                        and III and the stage III sample size from the
                        1000 Monte Carlo simulated functions of a
                        three-stage proteomis study, given a solution
                        of the design parameters
power.single.cost       Derive the averaged estimated costs of stage II
                        and III and the stage III sample size from the
                        1000 Monte Carlo simulated functions of a
                        three-stage proteomic study, given a solution
                        of the design parameters
power.t                 The power function used in the
                        optim.two.stage.single function
proteomicdesign-package
                        Optimization of a multi stage proteomic study
