protiq (version 1.2)

preprocessInputData.scampi: Precompute all quantities which will be used (repetitously) for further computations and do not depend on the parameter values.

Description

Build the bipartite graph, generate the list of connected components, store information about the graph structure for each nodes (e.g. number of neighbors or index of the connected components), optionally transform peptide abundance score.

Usage

"preprocessInputData"(scampiData, verbose = FALSE, ...)

Arguments

scampiData

Object of class scampi

verbose

If TRUE, detailed output is provided.

...

further arguments

Value

List

dataPrepro

object of class scampi

ppGraph

object of class graphNEL

ccList

list of connected components of ppGraph

See Also

runScampi, iterateScampi

Examples

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