baseline.peakDetection: Simultaneous Peak Detection and Baseline Correction

In baseline: Baseline Correction of Spectra

Simultaneous Peak Detection and Baseline Correction

Description

A translation from Kevin R. Coombes et al.'s MATLAB code for detecting peaks and removing baselines

Usage

baseline.peakDetection(spectra, left, right, lwin, rwin, snminimum,
mono=0, multiplier=5, left.right, lwin.rwin)

Arguments

spectra	Matrix with spectra in rows
left	Smallest window size for peak widths
right	Largest window size for peak widths
lwin	Smallest window size for minimums and medians in peak removed spectra
rwin	Largest window size for minimums and medians in peak removed spectra
snminimum	Minimum signal to noise ratio for accepting peaks
mono	Monotonically decreasing baseline if mono>0
multiplier	Internal window size multiplier
left.right	Sets eflt and right to value of left.right
lwin.rwin	Sets lwin and rwin to value of lwin.rwin

Details

Peak detection is done in several steps sorting out real peaks through different criteria. Peaks are removed from spectra and minimums and medians are used to smooth the remaining parts of the spectra. If snminimum is omitted, y3, midspec, y and y2 are not returned (faster)

Value

baseline	Matrix of baselines corresponding to spectra spectra
corrected	Matrix of baseline corrected spectra
peaks	Final list of selected peaks
sn	List signal to noise ratios for peaks
y3	List of peaks prior to singal to noise selection
midspec	Mid-way baseline estimation
y	First estimate of peaks
y2	Second estimate of peaks

Author(s)

Kristian Hovde Liland and Bjørn-Helge Mevik

References

KEVIN R. COOMBES et al.: Quality control and peak finding for proteomics data collected from nipple aspirate fluid by surface-enhanced laser desorption and ionization.

Examples

data(milk)
bc.peakDetection <- baseline(milk$spectra[1,, drop=FALSE], method='peakDetection',
	left=300, right=300, lwin=50, rwin=50)
## Not run: 
	plot(bc.peakDetection)

## End(Not run)

baseline documentation built on Nov. 18, 2023, 5:14 p.m.