protiq (version 1.2)

quantifyProteins: Compute the protein (and optionally the peptide) abundance scores.

Description

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

Usage

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

Arguments

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.

Value

Object of class scampi.

See Also

runScampi, iterateScampi

Examples

## 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)