# Automated MALDI Cell Assays Using Dose-Response Curve Fitting

## Documentation for package ‘MALDIcellassay’ version 0.4.47

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

Blank2022intmat | Blank2022intmat
Blank2022peaks | Blank2022peaks
Blank2022res | Blank2022res
Blank2022spec | Blank2022spec
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
getSinglePeaks | Extract peaks of single spectra spectra (before average calculation)
getSingleSpecIntensity | Extract the intensities of single spectra for a given mzIdx
getSNR | Extract SNR used for peak detection
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
MALDIassay-class | Class MALDIassay
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