locate.peaks {FTICRMS}R Documentation

Locate Peaks in a FT-ICR MS Spectrum

Description

Locates peaks in FT-ICR MS spectra assuming that the peaks are roughly parabolic on the log scale.

Usage

locate.peaks(peak.base, num.pts = 5, R2.thresh = 0.98, 
             oneside.min = 1, peak.method = "parabola", 
             thresh = -Inf)

Arguments

peak.base numeric matrix with two columns containing the masses and the pre-transformed spectrum intensities
num.pts minimum number of points needed to have a peak
R2.thresh minimum R^2 needed to have a peak
oneside.min minimum number of points needed on each side of the local maximum
peak.method how to locate peaks; currently the only options are "parabola" and "locmax"
thresh only local maxes that are larger than this will be checked to see if they are peaks

Details

If peak.method = "parabola", the algorithm works by locating local maxima in the spectrum, then seeing if any num.pts consecutive points with at least oneside.min point(s) on each side of the local maximum have a coefficient of determination (R^2) of at least R2.thresh when fitted with a quadratic. If, in addition, the coefficient of the squared term is negative, then this is declared a peak and the vertex of the corresponding parabola is located. The coordinates of the vertex give the components Center_hat and Max_hat in the return value. The Width_hat component is the negative reciprocal of the coefficient of the squared term.

If peak.method = "locmax", then the algorithm merely returns the set of local maxima, and the Width_hat component of the return value is NA.

Value

A data frame with columns

Center_hat estimated mass of peak
Max_hat estimated intensity of peak
Width_hat estimated width of peak

Note

An extremely large value for Width_hat most likely indicates a bad fit.

Using peak.method = "locmax" will vastly speed up the runtime, but may affect the quality of the analysis.

Author(s)

Don Barkauskas (barkda@wald.ucdavis.edu)

References

Barkauskas, D.A. et al. (2008) “Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data”. Submitted to Bioinformatics

See Also

run.peaks


[Package FTICRMS version 0.6 Index]