| NPA_fragmentationPeakDetection {IDSL.NPA} | R Documentation |
NPA Fragmentation Peaks Detection
Description
This function detects fragmentation peaks for the NPA analysis
Usage
NPA_fragmentationPeakDetection(input_MS_path, MSfilename, smoothingWindow,
peakHeightThreshold, minSNRbaseline, RTtolerance, nSpline, topRatioPeakHeight,
minIonRangeDifference, minNumNPApeaks, pearsonRHOthreshold, outputNPAeic = NULL,
number_processing_threads = 1)
Arguments
input_MS_path |
path to the MS files |
MSfilename |
MS file |
smoothingWindow |
number of scans for peak smoothing. |
peakHeightThreshold |
A minimum peak height threshold |
minSNRbaseline |
A minimum baseline S/N threshold |
RTtolerance |
retention time tolerance to detect common peaks |
nSpline |
number of points for further smoothing using a cubic spline smoothing method to add more points to calculate Pearson correlation rho values |
topRatioPeakHeight |
The top percentage of the chromatographic peak to calculate Pearson correlation rho values |
minIonRangeDifference |
Minimum distance (Da) between lowest and highest m/z to prevent clustering isotopic envelopes |
minNumNPApeaks |
Minumum number of ions in a NPA cluster |
pearsonRHOthreshold |
Minimum threshold for Pearson correlation rho values |
outputNPAeic |
When 'NULL' NPA EICs are not plotted. 'outputNPAeic' represents an address to save NPA EICs figures. |
number_processing_threads |
Number of processing threads for multi-threaded processing |
Value
A dataframe peaklist of co-detected NPA analysis.