NPA_fragmentationPeakDetection: NPA Fragmentation Peaks Detection

In IDSL.NPA: Nominal Peak Analysis (NPA)

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.

IDSL.NPA documentation built on July 9, 2023, 5:49 p.m.