integrateLinks: Integrating the new links to the PKN

In saezlab/CNORfeeder: Integration of CellNOptR to add missing links

Integrating the new links to the PKN

Description

This function integrates the new links inferred via the FEED method or from the database to the original PKN.

Usage

integrateLinks(feederObject = feederObject, cnolist = cnolist, database = NULL)

Arguments

feederObject	a feederObject structure, as produced by buildFeederObjectDynamic
cnolist	a cnolist structure, as produced by makeCNOlist
database	a database of interactions which can be optionally provided as an interaction matrix with 3 or 4 colums (source of interaction, sign of interaction, target of interaction and optionally a weight value from 0 to 1 indicating the significance of that interaction in the database). Default: database=NULL

Details

This function integrates the new links inferred via the FEED method or from the database to the original PKN. Moreover it indicates which are the integrated links and if a weighted database has been used it also shows the weights assigned to each integrated link. Links that are present in the original PKN are assigned a database weight of 0, integrated links that have been inferred via the FEED method and are not present in the database are assigned a database penalty of Inf, while integrated links present in the database take values between 0 and 1.

Value

this function returns a list with fields:

model	the integrated model
integLinksIdx	indices pointing towards the newly integrated links of the model
integSpeciesIdx	indices pointing towards the newly integrated species of the model
databaseWeight	weights assigned based on the presence of links in the database

Author(s)

E.Gjerga

Examples

data(feederObject_toy,package="CNORfeeder")
data(CNOlistToy_Gene, package="CNORfeeder")
data(CNOlistToy_Gene, package="CNORfeeder")

integratedModel = integrateLinks(feederObject = feederObject, cnolist = cnolist,
                                  database = NULL)

saezlab/CNORfeeder documentation built on Feb. 14, 2023, 3:23 p.m.