MALDIcellassay (version 0.4.47)

fitCurve: 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", "PQN", "median", "none"),
  SinglePointRecal = TRUE,
  verbose = TRUE
)

Value

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

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", "PQM", "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.

Examples

data(Blank2022spec)

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