Package index • MALDIcellassay

All functions

Blank2022intmat: Example intensity matrix from Blank 2022

Blank2022peaks: Example peaks from Blank 2022

Blank2022res: Example MALDIassay object from Blank 2022

Blank2022spec: Example spectra from Blank 2022

MALDIassay-class: Class MALDIassay

calculateChauvenetCriterion(): Calculate Chauvenet's criterion for outlier detection

calculateCurveFit(): Calculate the fit for a dose-response curve

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

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 is 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

shiftMassAxis(): Shift mass axis

transformConc2Log(): Convert concentration to log10 and replace zero's