calcPPS: Calculation of a peak picking score (PPS) by using natural,...

In rietho/IPO: Automated Optimization of XCMS Data Processing parameters

Calculation of a peak picking score (PPS) by using natural, stable 13C isotopes

Description

This function calculates PPS by identifying natural, stable 13C isotopes within an xcmsSet object. Peaks beeing part of an isotopologue are defined as reliable peaks (RP). Peaks which are not part of an isotopologue and where the intensity of possible isotopes is below a cutoff are defined as 'low intensity peaks' (LIP). PPS is then calculated by:
PPS = RP^2/(#all_peaks - LIP)

Usage

calcPPS(xset, isotopeIdentification, ...)

Arguments

xset	xcmsSet object
isotopeIdentification	This parameter defines the method for isotope identification. The method IPO was especially implemented for high resolution data. CAMERA is an established isotope and adduct annotation package.
...	Additional parameters to CAMERA's findIsotopes function.

Details

Calculation of a peak picking score (PPS) by using natural, stable 13C isotopes

Value

An array with 5 items:
1. Space for experimentid of the Design of Experiments (0 since not known in calcPPS)
2. Number of peaks
3. Number of peaks without LIP and RP
4. Reliable peaks (RP)
5. Peak picking score (PPS)

Author(s)

Gunnar Libiseller

See Also

findIsotopes.IPO findIsotopes.CAMERA

Examples

mzmlfile <- file.path(find.package("msdata"), "microtofq/MM14.mzML")
xset <- xcmsSet(mzmlfile, peakwidth=c(5,12), method="centWave")
calcPPS(xset)

rietho/IPO documentation built on Dec. 6, 2022, 8:17 a.m.