protiq (version 1.2)

getCovU: Compute covariance matrix of peptide abundances

Description

Compute the covariance matrix of the peptide abundances in the same connected component for given parameter values (beta and tau).

Usage

getCovU(cc, beta, tau)

Arguments

cc

pre-processed connected component (list)

beta

model parameter ("weight" of protein abundance contribution)

tau

model parameter (variance of error term)

Value

Same list as cc with an additional element named covU

See Also

quantifyProteins

Examples

## get data
data("leptoSRM")
## check input data
#dataChecked <- 
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)