ZvaluescasesVcontrolsPlots
                        A function for ploting the odds of being a case
                        vs control and their effects on adjustments for
                        confounders
ZvaluesfrommultinomPlots
                        A generic functon to plot Density of Z values
                        from a simulation from a multinomial population
                        using the balanced and unbalanced studies and a
                        3D representaion of the Z values
aclinicalProteomicsData-class
                        Class "aclinicalProteomicsData"
aclinicalProteomicsData-methods
                        S4 method for the aclinicalProteomicsData class
betweensampleVariance   A generic function for computing the biological
                        variance and mean differences between cases and
                        controls
betweensampleVariance-methods
                        Methods for Function betweensampleVariance
checkNo.replicates      A function to detect disparity in the number of
                        replicates across assays
clippda-package         A package for clinical proteomics profiling
                        data analysis
f                       A function to compute adjustments for the effct
                        of covariates (Z values) for an experiment with
                        a binary exposure and a binary confounder
fisherInformation       A generic function to compute the heterogeneity
                        correction factor in sample size calculations
fisherInformation-methods
                        Methods for Function fisherInformation
liverRawData            A dataframe of the protein expression data,
                        peak information and sample information
liver_pheno             A dataframe of phenotypic information
liverdata               A dataframe of the protein expression data,
                        peak information, and sample information
mostSimilarTwo          A function which indentifies two columns of a
                        matrix, or dataframe, with the highest pairwise
                        positive correlations
negativeIntensitiesCorrection
                        A function to correct the data for the negative
                        intensities caused by the normalization and
                        background correction procedures of mass
                        spectrometry data
phenoDataFrame          A generic function to set classes for the
                        variables in the dataframe of phenotypic
                        information.
pheno_urine             A dataframe of phenotypic information
preProcRepeatedPeakData
                        A function to pre-process repeated raw peak
                        data
proteomicsExprsData     A generic fuction to extract duplicate SELDI
                        data from an object of aclinicalProteomicsData
                        class in the same format as the data from
                        Biomarkers wizard
proteomicsExprsData-methods
                        Methods for Function proteomicsExprsData
proteomicspData         A function to extract a dataframe of phenotypic
                        information from an object of
                        aclinicalProteomicsData class
proteomicspData-methods
                        Methods for Function proteomicspData
replicateCorrelations   A generic function to compute intraclass
                        correlations
replicateCorrelations-methods
                        Methods for Function replicateCorrelations
sampleClusteredData     A function to arrange the data in sample-wise
                        pairs
sampleSize              A function for sample size calculations
sampleSize-methods      ~~ Methods for Function sampleSize
sampleSize3DscatterPlots
                        A function for 3D display of sample size in a
                        multi parameter space
sampleSizeContourPlots
                        A function to construct a grid with contours
                        for calculating sample size in multi
                        dimensional parameter space
sampleSizeParameters    A generic function to calculate sample size
                        parameters
sampleSizeParameters-methods
                        ~~ Methods for Function sampleSizeParameters
sample_technicalVariance
                        A generic function for computing the technical
                        variance
sample_technicalVariance-methods
                        Methods for Function sample_technicalVariance
show,aclinicalProteomicsData-method
                        Methods for Function show in Package 'methods'
spectrumFilter          A function to filter out samples with
                        conflicting pair-wise compound information
ztwo                    A function to compute Z values when there are
                        no covariates other than the cancer class
