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"' |