Man pages for MALDIcellassay
Automated MALDI Cell Assays Using Dose-Response Curve Fitting
| 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... |
| 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... |
| 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... |
| 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 |
