msQuantifyCount {msProcess}R Documentation

Count of Spectral Peaks Associated with a Peak Class

Description

Using the peak.list element of a given msSet object, this function returns a count of peaks associated with a common set of peak classes.

Usage

msQuantifyCount(x, xnew=NULL)

Arguments

x An object of class msSet containing a peak.class element.
xnew An object of class msSet. This object may contain a set of spectra that were not used to originally generate the peak classes. If the user wishes to quantify the original spectra, set xnew=NULL. Default: NULL.

Value

The same input msSet object (x if xnew=NULL, xnew otherwise) with an updated/new peak.matrix element. The rows and columns of the peak.matrix are the peak class measures and peak classes, respectively. If measure="count", the element "peak.list" is also updated with a class ID for each peak.

References

Morris, J.S., Coombes, K.R., Koomen, J., Baggerly, K.A., Kobayashi, R., ``Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum," Bioinformatics, 21(9):1764–75, 2005.

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

msQuantify, msQuantifyIntensity.


[Package msProcess version 1.0.5 Index]