msQuantifyIntensity {msProcess} | R Documentation |
Given an msSet
object, this function quantifies the spectral peak
intensities associated with a common set of peak classes.
The measure used to identify candidate peaks is the maximum intensity value
found over a pre-defined span of the corresponding peak class.
msQuantifyIntensity(x, xnew=NULL)
x |
An object of class msSet containing the 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 . |
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.
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.