getCovU: Compute covariance matrix of peptide abundances

In protiq: Protein (identification and) quantification based on peptide evidence

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

Note

This function is called by higher level functions (quantifyProteins). Calling it directly is seldomly necessary.

Author(s)

Sarah Gerster [e-mail]

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)

protiq documentation built on May 2, 2019, 9:06 a.m.