Package: MALDIcellassay 0.4.47.9000

Thomas Enzlein

MALDIcellassay: Automated MALDI Cell Assays Using Dose-Response Curve Fitting

Conduct automated cell-based assays using Matrix-Assisted Laser Desorption/Ionization (MALDI) methods for high-throughput screening of signals responsive to treatments. The package efficiently identifies high variance signals and fits dose-response curves to them. Quality metrics such as Z', V', log2 Fold-Change, and Curve response score (CRS) are provided for evaluating the potential of signals as biomarkers. The methodologies were introduced by Weigt et al. (2018) <doi:10.1038/s41598-018-29677-z> and refined by Unger et al. (2021) <doi:10.1038/s41596-021-00624-z>.

Authors:Thomas Enzlein [aut, cre, cph]

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MALDIcellassay.pdf |MALDIcellassay.html✨
MALDIcellassay/json (API)
NEWS

# Install 'MALDIcellassay' in R:
install.packages('MALDIcellassay', repos = c('https://cemos-mannheim.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cemos-mannheim/maldicellassay/issues

Datasets:

On CRAN:

cell-based-assayconcentration-response-analysismaldi-tof-msmass-spectrometryuntargeted-metabolomics

4.74 score 10 scripts 132 downloads 43 exports 46 dependencies

Last updated 1 months agofrom:4d64382155. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

Exports:calculateChauvenetCriterioncalculateCurveFitcalculateSSMDcalculateVPrimecalculateZPrimecheckRecalibrationextractIntensityextractSpotsfilterVariancefitCurvegetAllMzgetAppliedMzShiftgetAppliedNormFactorsgetAvgPeaksgetAvgSpectragetBinTolgetConcgetCurveFitsgetFittingParametersgetIntensityMatrixgetMzFromMzIdxgetMzShiftgetNormFactorsgetNormMethodgetNormMzgetNormMzTolgetPeakStatisticsgetRecalibrationErrorgetSinglePeaksgetSingleSpecIntensitygetSNRgetSpotsgetVarFilterMethodisMALDIassayloadSpectraloadSpectraMzMLnormalizenormalizeByFactorpeaks2dfplotCurvesplotPeakshiftMassAxistransformConc2Log

Dependencies:base64encclicolorspacecpp11digestdplyrfansifarverforcatsgenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMALDIquantMALDIquantForeignMASSMatrixmgcvmunsellnlmenplrpillarpkgconfigpurrrR6RColorBrewerreadBrukerFlexDatareadMzXmlDatarlangscalesstringistringrsvMisctibbletidyrtidyselectutf8vctrsviridisLitewithrXML

MALDI cell based assay Example

Rendered fromExample.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-09-01
Started: 2021-03-30

Readme and manuals

Help Manual

Help pageTopics
Example intensity matrix from Blank 2022Blank2022intmat
Example peaks from Blank 2022Blank2022peaks
Example MALDIassay object from Blank 2022Blank2022res
Example spectra from Blank 2022Blank2022spec
Calculate Chauvenet's criterion for outlier detectioncalculateChauvenetCriterion
Calculate the fit for a dose-response curvecalculateCurveFit
Calculate strictly standardized mean difference (SSMD)calculateSSMD
Calculate V'-FactorcalculateVPrime
Calculate Z'-factor of assay qualitycalculateZPrime
Check the recalibration of spectra from a MALDIassay objectcheckRecalibration
Extract intensity using peaks as templateextractIntensity
Extract the spot coordinatesextractSpots
Filter for high variance signalsfilterVariance
Fit dose-response curvesfitCurve
Get all mz value of an MALDIassay-objectgetAllMz
Extract applied mz-shiftgetAppliedMzShift
Extract applied normalization factorsgetAppliedNormFactors
Extract peaks of average spectragetAvgPeaks
Extract average spectragetAvgSpectra
Get binning tolerancegetBinTol
Extract the concentrations used in a MALDIassaygetConc
Extract curve fitsgetCurveFits
Get fitting parametersgetFittingParameters
Get the intensity matrix of single spectra for all fitted curvesgetIntensityMatrix
Get the mz value associated with a mzIdxgetMzFromMzIdx
Get mass shift for target mzgetMzShift
Get normalization factors from peak data.framegetNormFactors
Extract normalization methodgetNormMethod
Extract m/z used for normalizationgetNormMz
Extract tolerance used for normalizationgetNormMzTol
Extract peak statisticsgetPeakStatistics
Calculate remaining calibration error of a MALDIassay objectgetRecalibrationError
Extract peaks of single spectra spectra (before average calculation)getSinglePeaks
Extract the intensities of single spectra for a given mzIdxgetSingleSpecIntensity
Extract SNR used for peak detectiongetSNR
Get the spot coordinates of spectragetSpots
Extract variance filtering methodgetVarFilterMethod
Check if object is of class MALDIassayisMALDIassay
load bruker MALDI target plate spectraloadSpectra
load mzML spectraloadSpectraMzML
Class MALDIassayMALDIassay-class
Normalize spectra and peaksnormalize
Apply normalization factors to spectranormalizeByFactor
Convert a list of peaks to a data.framepeaks2df
generate ggplot objects for each of the curve fits in a MALDIassay objectplotCurves
Plot a peak of interest from a MALDIassay objectplotPeak
Shift mass axisshiftMassAxis
Convert concentration to log10 and replace zero'stransformConc2Log