acquisitionDirectory    Create a table containg the classes of the
                        acquisition.
analyzeAcquisitionFIA   Wrapper function for the full FIA analysis
                        workflow.
determiningSizePeak.Geom
                        Determine the limits of the injection peak in a
                        FIA acquisition.
estimateNoiseListFiles
                        Estimate the noise of multiple MS acquisition.
exportDataMatrix,proFIAset-method
                        Export data matrix.
exportExpressionSet,proFIAset-method
                        Export proFIAset to ExpressionSet
exportPeakTable,proFIAset-method
                        Export proFIAset as a peak table.
exportSampleMetadata,proFIAset-method
                        Export samples metadata.
exportVariableMetadata,proFIAset-method
                        Export variable metadata.
fillPeaks.WKNN,proFIAset-method
                        Fill missing values in the peak table.
findBandsFIA            Detect band in a FIA acquisition
findFIASignal           Detect peaks in an FIA acquisition.
findMzGroup,proFIAset-method
                        find a group in a FIA experiment.
getInjectionPeak        Fit an injection peak to an FIA acquisition.
group.FIA,proFIAset-method
                        Group the peaks of an FIA acquisition.
makeDataMatrix,proFIAset-method
                        Construct the data matrix of a proFIAset
                        object.
noiseEstimation-class   An S4 class to represent heteroscedasctic noise
                        of MS.
peaksGroup,proFIAset-method
                        Return the peaks corresponding to a group.
plotEICs,proFIAset-method
                        Plot raw temporal profiles of the selected
                        group.
plotInjectionPeaks,proFIAset-method
                        Plot the injection peaks of a proFIAset object.
plotNoise               Plot the estimated noise from a proFIAset
                        object.
plotRaw,proFIAset-method
                        plotting of raw data
proFIA-package          Process FIA-HRMS datasets.
proFIAset               Process FIA experiment.
proFIAset-class         An S4 class to represent an FIA experiments.
