msPeakSimple: Peak Detection via Local Maxima

In zeehio/msProcess: Protein Mass Spectra Processing

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.

zeehio/msProcess documentation built on May 4, 2019, 10:15 p.m.