msPeakSearch {msProcess} | R Documentation |
This method seeks intensities that are higher than those in a local area and are higher than an estimated average background at the sites.
msPeakSearch(x, y, noise.local=NULL, span=41, span.supsmu=0.05, snr.thresh=2, process="msPeakSearch")
x |
A numeric vector representing the m/z values of a spectrum. |
y |
A numeric vector representing the intensity values of the spectrum. |
noise.local |
A numeric 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: "msPeakSearch" . |
snr.thresh |
A numeric 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. Default: 41. |
span.supsmu |
The fraction of observations in the smoothing window. If span="cv" ,
then automatic (variable) span selection is done by means of cross validation.
Default: 0.05. |
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"
).
Tibshirani, R., Hastie, T., Narasimhan, B., Soltys, S., Shi, G., Koong, A., and Le, Q.T., ``Sample classification from protein mass spectrometry, by peak probability contrasts," Bioinformatics, 20(17):3034–44, 2004.
Yasui, Y., McLerran, D., Adam, B.L., Winget, M., Thornquist, M., Feng, Z., ``An automated peak identification/calibration procedure for high-dimensional protein measures from mass spectrometers," Journal of Biomedicine and Biotechnology, 2003(4):242–8, 2003.
Yasui, Y., Pepe, M., Thompson, M.L., Adam, B.L., Wright, Jr., G.L., Qu, Y., Potter, J.D., Winget, M., Thornquist, M., and Feng, Z., ``A data-analytic strategy for protein biomarker discovery: Profiling of high-dimensional proteomic data for cancer detection," Biostatistics, 4(3):449–63, 2003.
msPeak
, msPeakSimple
, msExtrema
, peaks
.