protiq: Protein (identification and) quantification based on peptide evidence

Method for protein quantification based on identified and quantified peptides. protiq can be used for absolute and relative protein quantification. Input peptide abundance scores can come from various sources, including SRM transition areas and intensities or spectral counts derived from shotgun experiments. The package is still being extended to also include the model for protein identification, MIPGEM, presented in Gerster, S., Qeli, E., Ahrens, C.H. and Buehlmann, P. (2010). Protein and gene model inference based on statistical modeling in k-partite graphs. Proceedings of the National Academy of Sciences 107(27):12101-12106.

Install the latest version of this package by entering the following in R:
AuthorSarah Gerster and Peter Buehlmann
Date of publication2013-08-19 01:00:26
LicenseGPL (>= 2)

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checkInputData Man page
checkInputData.scampi Man page
estimateModelParameters Man page
getCovU Man page
iterateScampi Man page
leptoSRM Man page
leptoSRMedgespp Man page
leptoSRMpeptides Man page
leptoSRMproteins Man page
plot,scampi,missing-method Man page
plot,scampiVal,missing-method Man page
preprocessInputData Man page
preprocessInputData.scampi Man page
protiq Man page
protiq-package Man page
quantifyPeptide Man page
quantifyProtein Man page
quantifyProteins Man page
runScampi Man page
scampi Man page
scampi-class Man page
scampiVal Man page
scampiVal-class Man page
show,scampi-method Man page
show,scampiVal-method Man page
summary,scampi-method Man page
summary,scampiVal-method Man page

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