recursiveMZpeaklistCorrector: recursive mass correction

In IDSL.IPA: Intrinsic Peak Analysis (IPA) for HRMS Data

recursive mass correction

Description

This function performs recursive mass correction.

Usage

recursiveMZpeaklistCorrector(peaklist, spectraScan, scanTolerance,
aggregatedSpectraList, retentionTime, massAccuracy, smoothingWindow,
peakResolvingPower, minNIonPair, minPeakHeight, minRatioIonPair, maxRPW,
minSNRbaseline, maxR13CcumulatedIntensity, maxPercentageMissingScans, nSpline,
exportEICparameters = NULL, number_processing_threads = 1)

Arguments

peaklist	an IPA peaklist from 'primaryXICdeconvoluter' function.
spectraScan	a matrix consists of 5 columns. The column contents are the m/z of 12C isotopologues, intensity of 12C isotopologues, scan number (t), m/z of 13C isotopologues, and intensity of 13C isotopologues.
scanTolerance	a scan tolerance to extend the chromatogram for better calculations.
aggregatedSpectraList	aggregated spectraList and spectra matrix from the 'IPA_spectraListAggregator' module
retentionTime	a vector of retention times for corresponding scan numbers.
massAccuracy	an m/z value to perform chromatography analysis.
smoothingWindow	a number of scans for peak smoothing.
peakResolvingPower	a value to represent peak resolving power.
minNIonPair	minimum number of nIsoPair for an individual peak.
minPeakHeight	minimum peak height for an individual peak.
minRatioIonPair	minimum ratio of nIsoPair per number of available scans within an individual peak.
maxRPW	maximum allowed value of ratio of peak width at half-height to baseline (RPW) for an individual peak.
minSNRbaseline	minimum S/N baseline for an individual peak.
maxR13CcumulatedIntensity	maximum allowed value of average R13C for an individual peak.
maxPercentageMissingScans	maximum allowed value of percentage missing scans on the raw chromatogram for an individual peak.
nSpline	number of points for further smoothing using a cubic spline smoothing method to calculate ancillary chromatographic parameters.
exportEICparameters	When ‘NULL', EICs are not plotted. 'exportEICparameters' should contain three variables of 1) an address to save IPA EICs figures, 2) ’HRMS' file name, and 3) a valid string of characters.
number_processing_threads	number of processing threads

Value

a dataframe consisting of 24 columns representing chromatography and mass spectrometry parameters. Each row represents an individual separated chromatographic peak.

IDSL.IPA documentation built on June 7, 2023, 6:01 p.m.