| primaryXICdeconvoluter {IDSL.IPA} | R Documentation |
Primary peak analyzer
Description
This function performs the first round of the chromatography analysis.
Usage
primaryXICdeconvoluter(spectraScan, scanTolerance, indexXIC, aggregatedSpectraList,
retentionTime, massAccuracy, smoothingWindow, peakResolvingPower, minNIonPair,
minPeakHeight, minRatioIonPair, maxRPW, minSNRbaseline, maxR13CcumulatedIntensity,
maxPercentageMissingScans, nSpline, exportEICparameters = NULL,
number_processing_threads = 1)
Arguments
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. |
indexXIC |
a list of indices of candidate 12C m/z values from spectraScan matrix. |
aggregatedSpectraList |
aggregated spectraList and spectra matrix from the 'IPA_spectraListAggregator' module |
retentionTime |
a vector of retention times vs. corresponding scan numbers. |
massAccuracy |
a m/z value to perform chromatography analysis. |
smoothingWindow |
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. |
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 data frame consisting of 24 columns representing chromatography and mass spectrometry parameters. Each row represents an individual separated chromatographic peak.