preprocessInputData.scampi: Precompute all quantities which will be used (repetitously)...

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

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

## S3 method for class 'scampi'
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

Note

This function is called by one of the main functions of the package, runScampi. Calling this function directly is seldomly necessary.

Author(s)

Sarah Gerster [e-mail]

See Also

runScampi, iterateScampi

Examples

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

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