Protein (identification and) quantification based on peptide evidence

[Up] [Top]

Documentation for package ‘protiq’ version 1.2

Help Pages

protiq-package Protein (identification and) quantification based on peptide evidence
checkInputData Generic function to check if the input data fulfills all requirements for protein inference with MIPGEM or quantification with SCAMPI.
checkInputData.scampi Check if input object fulfills all requirements in order to proceed with the protein quantification step.
estimateModelParameters Estimate the SCAMPI model paramteres alpha, beta, mu and tau from the data
getCovU Compute covariance matrix of peptide abundances
iterateScampi SCAMPI protein quantification function with iterative outlier removal
leptoSRM SRM quantification example data
leptoSRMedgespp SRM quantification: edges informationu.
leptoSRMpeptides SRM quantification: peptide example data
leptoSRMproteins SRM quantification: protein example data
plot-method Class '"scampi"'
plot-method Class '"scampiVal"'
preprocessInputData Generic function to preprocess the input data for protein inference with MIPGEM or quantification with SCAMPI to speed up further computations.
preprocessInputData.scampi Precompute all quantities which will be used (repetitously) for further computations and do not depend on the parameter values.
protiq Protein (identification and) quantification based on peptide evidence
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 scores.
runScampi SCAMPI protein quantification function
scampi Class '"scampi"'
scampi-class Class '"scampi"'
scampiVal Class '"scampiVal"'
scampiVal-class Class '"scampiVal"'
show-method Class '"scampi"'
show-method Class '"scampiVal"'
summary-method Class '"scampi"'
summary-method Class '"scampiVal"'