msPeakSearch: Peak Detection via Elevated Intensity

In zeehio/msProcess: Protein Mass Spectra Processing

Description

This method seeks intensities that are higher than those in a local area and are higher than an estimated average background at the sites.

Usage

msPeakSearch(x, y, noise.local=NULL, span=41, span.supsmu=0.05,
    snr.thresh=2, process="msPeakSearch")

Arguments

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.

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

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.

See Also

msPeak, msPeakSimple, msExtrema, peaks.

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