buildFeederObjectDynamic {CNORfeeder} | R Documentation

## Building Feeder-Object for the integration to the PKN

### Description

This function estimates the possible mechanisms of interactions to be added to the PKN from a database of interactions for improving the fitting cost.

### Usage

    buildFeederObjectDynamic(model = model, cnolist = cnolist, indices = indices, database = NULL, DDN = TRUE, pathLength = 2, k = 2, measErr = c(0.1, 0), timePoint = NA)

### Arguments

`model` | a model as returned by readSIF. Alternatively, the filename can also be provided
`cnolist` | a cnolist structure, as produced by makeCNOlist
`indices` | a list of indices of poorly fitted measurements as returned from identifyMisfitIndices
`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
`DDN` | a parameter indicating whether integrating links inferred from the Data-Driven FEED approach. Default: DDN = TRUE
`pathLength` | a path length parameter for the maximal path length of additional interactions to search for in the database. Default: pathLength = 2
`k` | a parameter that determine the threshold of significancy of the effect of stimuli and inhibitors, default to 2
`measErr` | a 2 value vector (err1, err2) defining the error model of the data as sd^2 = err1^2 + (err2*data)^2, default to c(0.1, 0)
`timePoint` | time-points to be considered. By default set to NA, which means that the function will search for poorly fitted measurements at each time-point.

### Details

The function identifies and proposes the new links to integrate in the PKN either either by means of the data-driven method from the FEED algorithm or from the provided database of interactions or from both of them.

### Value

this function returns a list with fields:

`Original PKN` | the original PKN
`Feed mechanisms` | the list of proposed interactions to integrate to the PKN (if both the database and the data-driven method are considered by the user, the last mechanism corresponds to the data-driven approach)

### Author(s)

E.Gjerga

### Examples

    data(ToyModel_Gene, package="CNORfeeder")
    data(CNOlistToy_Gene, package="CNORfeeder")
    data(simData_toy,package="CNORfeeder")

    feederObject = buildFeederObjectDynamic(model = model, cnolist = cnolist,
                                            indices = NULL, database = NULL,
                                            DDN = TRUE, pathLength = 2)

[Package CNORfeeder version 1.28.0 Index]