msPeakSimple {msProcess} | R Documentation |
Performs peak detection via a simple local maxima search.
msPeakSimple(x, y, noise.local=NULL, span=3, snr.thresh=2, process="msPeakSimple")
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. |
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"
).
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.
msPeak
, msPeakSearch
, msExtrema
, peaks
.