PeakList {ptairMS} | R Documentation |
Detection and quantification of peaks on a sum spectrum.
PeakList( raw, mzNominal = unique(round(getRawInfo(raw)$mz)), ppm = 130, resolutionRange = c(3000, 5000, 8000), minIntensity = 5, fctFit = c("sech2", "averagePeak")[1], peakShape = NULL, maxIter = 1, R2min = 0.995, autocorNoiseMax = 0.3, plotFinal = FALSE, plotAll = FALSE, thNoiseRate = 1.1, minIntensityRate = 0.01, countFacFWHM = 10, daSeparation = 0.005, d = 3, windowSize = 0.4 ) ## S4 method for signature 'ptrRaw' PeakList( raw, mzNominal = unique(round(getRawInfo(raw)$mz)), ppm = 130, resolutionRange = c(300, 5000, 8000), minIntensity = 5, fctFit = c("sech2", "averagePeak")[1], peakShape = NULL, maxIter = 3, R2min = 0.995, autocorNoiseMax = 0.3, plotFinal = FALSE, plotAll = FALSE, thNoiseRate = 1.1, minIntensityRate = 0.01, countFacFWHM = 10, daSeparation = 0.005, d = 3, windowSize = 0.4 )
raw |
|
mzNominal |
the vector of nominal mass where peaks will be detected |
ppm |
the minimum distance between two peeks in ppm |
resolutionRange |
vector with resolution min, resolution Mean, and resolution max of the PTR |
minIntensity |
the minimum intenisty for peaks detection. The final
threshold for peak detection will be : max ( |
fctFit |
the function for the quantification of Peak, should be average or Sech2 |
peakShape |
a list with reference axis and a reference peak shape centered in zero |
maxIter |
maximum iteration of residual analysis |
R2min |
R2 minimum to stop the iterative residual analysis |
autocorNoiseMax |
the autocorelation threshold for Optimal windows
Savitzky Golay
filter in |
plotFinal |
boolean. If TRUE, plot the spectrum for all nominal masses, with the final fitted peaks |
plotAll |
boolean. Tf TRUE, plot all step to get the final fitted peaks |
thNoiseRate |
The rate which multiplies the max noise intensity |
minIntensityRate |
The rate which multiplies the max signal intensity |
countFacFWHM |
integer. We will sum the fitted peaks on a window's size of countFacFWHM * FWHM, centered in the mass peak center. |
daSeparation |
the minimum distance between two peeks in Da for nominal mass < 17. |
d |
the degree for the |
windowSize |
peaks will be detected only around m - windowSize ;
m + windowSize, for all
m in |
a list containing:
peak: a data.frame, with for all peak detected: the mass center, the
intensity count in cps, the peak width (delta_mz), correspond to the Full Width Half
Maximum (FWHM),the resolution m/delta_m, the other parameters values estimated
of fitFunc
.
warnings: warnings generated by the peak detection algorithm per nominal masses
infoPlot: elements needed to plot the fitted peak per nominal masses
library(ptairData) filePath <- system.file('extdata/exhaledAir/ind1', 'ind1-1.h5', package = 'ptairData') file <- readRaw(filePath) peakList <- PeakList(file, mzNominal = c(21,63)) peakList$peak