checkInputData.scampi: Check if input object fulfills all requirements in order to...

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

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

## S3 method for class 'scampi'
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

Object of class 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.

Author(s)

Sarah Gerster [e-mail]

See Also

scampi-class

Examples

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

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