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.

Author
Sarah Gerster and Peter Buehlmann
Date of publication
2013-08-19 01:00:26
Maintainer
ORPHANED
License
GPL (>= 2)
Version
1.2

View on CRAN

Man pages

checkInputData
Generic function to check if the input data fulfills all...
checkInputData.scampi
Check if input object fulfills all requirements in order to...
estimateModelParameters
Estimate the SCAMPI model paramteres alpha, beta, mu and tau...
getCovU
Compute covariance matrix of peptide abundances
iterateScampi
SCAMPI protein quantification function with iterative outlier...
leptoSRM
SRM quantification example data
leptoSRMedgespp
SRM quantification: edges informationu.
leptoSRMpeptides
SRM quantification: peptide example data
leptoSRMproteins
SRM quantification: protein example data
preprocessInputData
Generic function to preprocess the input data for protein...
preprocessInputData.scampi
Precompute all quantities which will be used (repetitously)...
protiq-package
Protein (identification and) quantification based on peptide...
quantifyPeptide
Compute expected value for the peptide abundance.
quantifyProtein
Compute expected value and variance of a protein abundance.
quantifyProteins
Compute the protein (and optionally the peptide) abundance...
runScampi
SCAMPI protein quantification function
scampi-class
Class '"scampi"'
scampiVal-class
Class '"scampiVal"'

Files in this package

protiq
protiq/tests
protiq/tests/test_scampi.R
protiq/NAMESPACE
protiq/data
protiq/data/leptoSRM.rda
protiq/R
protiq/R/scampi_classes.R
protiq/R/protiq.R
protiq/MD5
protiq/DESCRIPTION
protiq/man
protiq/man/checkInputData.scampi.Rd
protiq/man/quantifyPeptide.Rd
protiq/man/preprocessInputData.scampi.Rd
protiq/man/scampi-class.Rd
protiq/man/leptoSRMedgespp.Rd
protiq/man/checkInputData.Rd
protiq/man/leptoSRM.Rd
protiq/man/leptoSRMpeptides.Rd
protiq/man/quantifyProteins.Rd
protiq/man/quantifyProtein.Rd
protiq/man/leptoSRMproteins.Rd
protiq/man/getCovU.Rd
protiq/man/scampiVal-class.Rd
protiq/man/preprocessInputData.Rd
protiq/man/runScampi.Rd
protiq/man/iterateScampi.Rd
protiq/man/protiq-package.Rd
protiq/man/estimateModelParameters.Rd