getIntensityMatrix: Get the intensity matrix of single spectra for all fitted...

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

Get the intensity matrix of single spectra for all fitted curves

Description

Get the intensity matrix of single spectra for all fitted curves

Usage

getIntensityMatrix(object, avg = FALSE, excludeNormMz = FALSE)

Arguments

object	Object of class MALDIassay
avg	Logical, return single spectra intensity matrix (default) or average spectra intensity matrix
excludeNormMz	Logical, exclude normMz from intensity matrix.

Details

Note that the returned matrix only contains m/z values that were actually fitted. If a variance filtering step was applied this will not include all m/z values. If you wish to get a matrix of all m/z values use MALDIquant::intensityMatrix(getSinglePeaks(object)). For average spectra intensity matrix with all m/z values use MALDIquant::intensityMatrix(getAvgPeaks(object), getAvgSpectra(object)).

Value

A matrix with columns as m/z values and rows as concentrations/spectra

Examples

# see example for `fitCurve()` to see how this data was generated
data(Blank2022res)
head(getIntensityMatrix(Blank2022res, avg = TRUE, excludeNormMz = TRUE) )

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