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protiq (version 1.2)

Protein (identification and) quantification based on peptide evidence

Description

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.

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Version

Install

install.packages('protiq')

Monthly Downloads

49

Version

1.2

License

GPL (>= 2)

Maintainer

ORPHANED

Last Published

August 18th, 2013

Functions in protiq (1.2)

leptoSRMedgespp

SRM quantification: edges informationu.
quantifyProtein

Compute expected value and variance of a protein abundance.
checkInputData.scampi

Check if input object fulfills all requirements in order to proceed with the protein quantification step.
scampi-class

Class "scampi"
leptoSRMpeptides

SRM quantification: peptide example data
checkInputData

Generic function to check if the input data fulfills all requirements for protein inference with MIPGEM or quantification with SCAMPI.
preprocessInputData.scampi

Precompute all quantities which will be used (repetitously) for further computations and do not depend on the parameter values.
protiq-package

Protein (identification and) quantification based on peptide evidence
iterateScampi

SCAMPI protein quantification function with iterative outlier removal
estimateModelParameters

Estimate the SCAMPI model paramteres alpha, beta, mu and tau from the data
leptoSRMproteins

SRM quantification: protein example data
scampiVal-class

Class "scampiVal"
runScampi

SCAMPI protein quantification function
getCovU

Compute covariance matrix of peptide abundances
preprocessInputData

Generic function to preprocess the input data for protein inference with MIPGEM or quantification with SCAMPI to speed up further computations.
leptoSRM

SRM quantification example data
quantifyProteins

Compute the protein (and optionally the peptide) abundance scores.
quantifyPeptide

Compute expected value for the peptide abundance.