Blank2022intmat         Blank2022intmat
Blank2022peaks          Blank2022peaks
Blank2022res            Blank2022res
Blank2022spec           Blank2022spec
MALDIassay-class        Class MALDIassay
calculateChauvenetCriterion
                        Calculate Chauvenet's criterion for outlier
                        detection
calculateCurveFit       Calculate the fit for a dose-response curve
calculatePeakStatistics
                        Calculate peak statistics
calculateSSMD           Calculate strictly standardized mean difference
                        (SSMD)
calculateVPrime         Calculate V'-Factor
calculateZPrime         Calculate Z'-factor of assay quality
checkRecalibration      Check the recalibration of spectra from a
                        MALDIassay object
extractIntensity        Extract intensity using peaks as template
extractSpots            Extract the spot coordinates
filterVariance          Filter for high variance signals
fitCurve                Fit dose-response curves
getAllMz                Get all mz value of an MALDIassay-object
getAppliedMzShift       Extract applied mz-shift
getAppliedNormFactors   Extract applied normalization factors
getAvgPeaks             Extract peaks of average spectra
getAvgSpectra           Extract average spectra
getBinTol               Get binning tolerance
getConc                 Extract the concentrations used in a MALDIassay
getCurveFits            Extract curve fits
getDirectory            Extract directory path
getFittingParameters    Get fitting parameters
getIntensityMatrix      Get the intensity matrix of single spectra for
                        all fitted curves
getMzFromMzIdx          Get the mz value associated with a mzIdx
getMzShift              Get mass shift for target mz
getNormFactors          Get normalization factors from peak data.frame
getNormMethod           Extract normalization method
getNormMz               Extract m/z used for normalization
getNormMzTol            Extract tolerance used for normalization
getPeakStatistics       Extract peak statistics
getRecalibrationError   Calculate remaining calibration error of a
                        MALDIassay object
getSNR                  Extract SNR used for peak detection
getSinglePeaks          Extract peaks of single spectra spectra (before
                        average calculation)
getSingleSpecIntensity
                        Extract the intensities of single spectra for a
                        given mzIdx
getSpots                Get the spot coordinates of spectra
getVarFilterMethod      Extract variance filtering method
isMALDIassay            Check if object if of class MALDIassay
loadSpectra             load bruker MALDI target plate spectra
loadSpectraMzML         load mzML spectra
normalize               Normalize spectra and peaks
normalizeByFactor       Apply normalization factors to spectra
peaks2df                Convert a list of peaks to a data.frame
plotCurves              generate ggplot objects for each of the curve
                        fits in a MALDIassay object
plotPeak                Plot a peak of interest from a MALDIassay
                        object
sdMassSpectrum          Compute standard-deviation spectra
shiftMassAxis           Shift mass axis
transformConc2Log       Convert concentration to log10 and replace
                        zero's
