Description Usage Arguments Value References See Also
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.
1 | msQuantifyIntensity(x, xnew=NULL)
|
x |
An object of class |
xnew |
An object of class |
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.
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