fitCurve: Fit dose-response curves

In CeMOS-Mannheim/MALDIcellassay: Automated MALDI Cell Assays Using Dose-Response Curve Fitting

Fit dose-response curves

Description

Fit dose-response curves

Usage

fitCurve(
  spec,
  unit = c("M", "mM", "uM", "nM", "pM", "fM"),
  varFilterMethod = c("mean", "median", "q25", "q75", "none"),
  monoisotopicFilter = FALSE,
  averageMethod = c("mean", "median", "sum"),
  normMz = NULL,
  normTol = 0.1,
  alignTol = 0.01,
  binTol = 2e-04,
  SNR = 3,
  halfWindowSize = 3,
  allowNoMatches = TRUE,
  normMeth = c("mz", "TIC", "median", "none"),
  SinglePointRecal = TRUE,
  verbose = TRUE
)

Arguments

spec	List of MALDIquant::MassSpectrum
unit	Character, unit of concentration. Used to calculate the concentration in Moles so that pIC50 is correct. Set to "M" if you dont want changes in your concentrations.
varFilterMethod	Character, function applied for high variance filtering. One of the following options mean (default), median, q25, q75 or none (no filtering).
monoisotopicFilter	Logical, filter peaks and just use monoisotopic peaks for curve fit.
averageMethod	Character, aggregation method for average mass spectra ("mean" or "median")
normMz	Numeric, mz used for normalization AND for single point recalibration.
normTol	Numeric, tolerance in Dalton to match normMz
alignTol	Numeric, tolerance for spectral alignment in Dalton.
binTol	Numeric, tolerance for binning of peaks.
SNR	Numeric, signal to noise ratio for peak detection.
halfWindowSize	2ction. See MALDIquant::detectPeaks().
allowNoMatches	Logical, if normMz can not be found in a spectrum, proceed and exclude spectrum or stop
normMeth	Character, normalization method. Can either be "TIC", "median" or "mz". If "mz" then the normMz is used. If none no normalization is done.
SinglePointRecal	Logical, perform single point recalibration to normMz
verbose	Logical, print logs to console.

Value

Object of class MALDIassay. The most important slot is fits which contains the IC50 curve fits.

Examples

data(Blank2022spec)

fitCurve(spec = Blank2022spec,
         SinglePointRecal = TRUE, 
         normMz = 760.585, 
         alignTol = 0.1, 
         normTol = 0.1,
         varFilterMethod = "mean") 

CeMOS-Mannheim/MALDIcellassay documentation built on Jan. 24, 2025, 11:17 p.m.