accum                   Response calculation
addIonSatistics         Summary statistics - Ion intensities per
                        spectra
addLoadings             Adjust for confounding - add an appropiate
                        target
addRetentionAtApex      Summary statistics - Calculates retention time
                        statistics at apex
addRetentionIndexTimeStatistics
                        Summary statistics - Calculates index retention
                        time statistics
adjustBy                Adjust for confounding - Generic function for
                        centring data
adjustOne               Adjust for confounding - In one single
                        experiment only
adjusting               Adjust for confounding - State of the art
                        adjustments for confounding
avrgLoading             Adjust for confounding - calculates the average
                        loading
channelResponses        Response calculation
copyLoadings            Adjust for confounding - copy loadings from one
                        experiment to another
factoring               Sample design - Generating multiple factor
                        designs from one-dimensional factor
meetSelection           Data parsing - from Proteom Discover v1.4
mergeFrames             Merging multiple experiments
norm2Reference          Response calculation
pAction                 Plotting p-value distributions
pRetention              Plot Retention Time Statistics
pVioline                Plot Retention Time Statistics in violine form
pVolcano                Volcano plot
plotMePeptide           Plot interaction plots of peptides
plotMeProtein           Plot interaction plots of proteins
responseStatisics       Summary statistics - Generic to calculate
                        summary statistics
selectByConfidence      Result filtering - Test for biological effect
selectByEffect          Result filtering - Test for biological effect
selectByFDR             Result filtering
testForPeptideEffect    Data Analysis - Testing on peptide level
testForProteinEffect    Data Analysis - Testing on protein level
testing                 Data Analysis - Testing features with Tukey
                        Honest Significant Differences
testingOneshot          Data Analysis - Testing one feature without
                        Tukey Honest Significant Differences
testingTukey            Data Analysis - Testing one feature with Tukey
                        Honest Significant Differences
toAlpha                 Measuring stability - angle of loading vector
toProportions           Transformation - From intensity scales to
                        density histrograms
