Get the intensity matrix of single spectra for all fitted curves

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.

Value

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

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)).

Examples

# see example for `fitCurve()` to see how this data was generated
data(Blank2022res)
head(getIntensityMatrix(Blank2022res, avg = TRUE, excludeNormMz = TRUE) )
#> Warning: Could not find normMz. No exlusion possible.
#> [1] NA NA NA NA NA NA