protiq (version 1.2)

checkInputData.scampi: Check if input object fulfills all requirements in order to proceed with the protein quantification step.

Description

The dataframes contained in the input object are tested for completeness and consistency. It ensures that the input data is suited to build the bipartite graph and holds all needed variables for parameter estimation, prediction of protein quantities and peptide abundance reassessment. If some optional variables are missing, the dataframes are completed with default values.

Usage

"checkInputData"(scampiData, rescaling = TRUE, verbose = FALSE, ...)

Arguments

scampiData

object of class scampi-class

rescaling

If TRUE, the peptide abundance scores are logarithmized (log10). If this transformation has not yet been done during preprocessing, it is strongly recommended to stick to the default: rescaling=TRUE.

verbose

if TRUE, basic information are printed to indicate the progress of the function

...

further arguments

Value

scampi-class containing the checked, and possily completed, dataframes. If the input data does not match the requirements, the function exits with an error message.

See Also

scampi-class

Examples

data("leptoSRM")
dataChecked <- checkInputData(scampi(peptides=leptoSRMpeptides,
                                     proteins=leptoSRMproteins, 
                                     edgespp=leptoSRMedgespp),
                              rescaling=FALSE)