msPeakSimple {msProcess}R Documentation

Peak Detection via Local Maxima

Description

Performs peak detection via a simple local maxima search.

Usage

msPeakSimple(x, y, noise.local=NULL, span=3,
    snr.thresh=2, process="msPeakSimple")

Arguments

x A vector representing the m/z values of a spectrum.
y A vector representing the intensity values of the spectrum.
noise.local A vector representing the estimated local noise level. Default: NULL.
process A character string denoting the name of the process to register with the (embedded) event history object of the input after processing the input data. Default: "msPeakSimple".
snr.thresh A value representing the signal to noise threshold. Only the local maxima whose signal to noise level is above this value will be recorded as peaks. Default: 2.
span A peak is defined as an element in a sequence which is greater than all other elements within a window of width span centered at that element. The default value is span=3, meaning that a peak is bigger than both of its neighbors.

Value

A data.frame with 10 columns: peak class location, left bound, right bound and peak span in both clock tick ("tick.loc", "tick.left", "tick.right", "tick.span") and mass measure ("mass.loc", "mass.left", "mass.right", "mass.span"), and peak signal-to-noise ratio and intensity ("snr", "intensity"). If noise.local is NULL, "snr" is the same as ("intensity").

References

Coombes, K.R., Tsavachidis, S., Morris, J.S., Baggerly, K.A., Kuerer, H.M., ``Improved peak detection and quantification of mass spectrometry data acquired from surface-enhanced laser desorption and ionization by denoising spectra with the undecimated discrete wavelet transform," Proteomics, 5:4107–17, 2005.

See Also

msPeak, msPeakSearch, msExtrema, peaks.


[Package msProcess version 1.0.5 Index]