getPIC.kmeans: Extract PICs from a LC-MS raw object based on optimal k-means...

In hcji/KPIC2: Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms

Extract PICs from a LC-MS raw object based on optimal k-means clustering.

Description

This method bases on the optimal k-means clustering of m/z values of data points in ROI. see reference for details.

Usage

getPIC.kmeans(raw, level, mztol = 0.1, gap = 3, width = c(5, 60), alpha = 0.3, min_snr = 4, ...)

Arguments

raw	Raw LC-MS data object obtained by LoadData function.
level	Mass traces are only retained if their maximum values are over level.
mztol	The m/z range of ROI.
gap	The number of gap points of a mass trace.
width	The range of a mass trace.
alpha	The parameter of forecasting.
min_snr	Minimum signal to noise ratio.
...	No use at present.

Value

a LIST of:

scantime	The retention time of each scan.
pics	The extracted mass trace.
peaks	The detected peak of each mass trace.

References

Ji, H., et al. "KPIC2: An Effective Framework for Mass Spectrometry-Based Metabolomics Using Pure Ion Chromatograms." Analytical Chemistry (2017).

See Also

getPIC

hcji/KPIC2 documentation built on Aug. 23, 2022, 1:42 p.m.