quantifyProteins: Compute the protein (and optionally the peptide) abundance...
In protiq: Protein (identification and) quantification based on peptide evidence

Description Usage Arguments Value Note Author(s) See Also Examples

Compute the protein (and optionally the peptide) abundance scores for all proteins given the specified parameter values

1 2	quantifyProteins(scampiData, ccList, paramList, quantifyPeptides = FALSE, verbose = FALSE)

`scampiData`	Object of class `scampi`
`ccList`	List of pre-processed connected components
`paramList`	Named list of vectors with at least four named elements: `alphaH`, `betaH`, `muH` and `tauH` (estimates for the four model parameters). The name of list element corresponds to the parameter estimation method, namely `LSE` or `MLE`.
`quantifyPeptides`	If TRUE, also compute peptide abundance scores/residuals.
`verbose`	If `TRUE`, detailed output is provided.

Object of class scampi.

This function is intended to quantify (a subset of) proteins and reassess peptide scores when the parameter values have already been computed previously. To run a whole analysis (check input data, preprocess connected components, estimate model parameters and compute abundance sore estimates) you should use the function runScampi or iterateScampi.

Sarah Gerster sarah.gerster@isb-sib.ch

runScampi, iterateScampi

## get data
data("leptoSRM")
## check input data
dataChecked <- checkInputData(scampiData=scampi(peptides=leptoSRMpeptides, 
                                                proteins=leptoSRMproteins, 
                                                edgespp=leptoSRMedgespp),
                              rescaling=FALSE)
## preprocess input data
tmpPrepro <- preprocessInputData(scampiData=dataChecked)
dataPrepro <- tmpPrepro[["dataPrepro"]]
myCCList <- tmpPrepro[["ccList"]]
rm(tmpPrepro)

## compute covariance matrices
myCCList <- lapply(myCCList, getCovU,
                   beta=0.2,
                   tau=0.5)

## compute protein and peptide abundance scores
scampiRes <- 
  quantifyProteins(scampiData=dataPrepro, ccList=myCCList, 
                   paramList=list(LSE=c(alphaH=0, betaH=0.2, muH=0.3, 
                                        tauH=0.2)),
                   quantifyPeptides=FALSE)