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

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/protiq.R

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

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## 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 sarah.gerster@isb-sib.ch

See Also

runScampi, iterateScampi

Examples

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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.