integrateLinks {CNORfeeder} | R Documentation

## 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)

[Package CNORfeeder version 1.28.0 Index]