writeFuzzyNetwork: Despict the network results of training a cFL model to data...

In saezlab/CNORfuzzy: Addon to CellNOptR: Fuzzy Logic

Description

Fuzzy network results output.

Usage

writeFuzzyNetwork(postRefThresh, allFinalMSEs, allRes, tag=NULL,verbose=FALSE)

Arguments

postRefThresh	Post refinement threshold (selection threshold) chosen from plot produced by compileMultiRes
allFinalMSEs	matrix containing MSEs produced by compileMultiRes
allRes	list containing all results produced by compileMultiRes
tag	String to include in filename of pdf plot
verbose	If extra warnings should be displayed

Details

The weights of the edges are computed as the mean across models using post refinement threshold (selection threshold) to choose reduced refined model resulting from each run.

As with writeNetwork, this function maps back the edges weights from the optimised (expanded and compressed) model to the original model. The mapping back only works if the path has length 2 at most (i.e. you have node1-comp1-comp2-node2, where comp refer to nodes that have been compressed).

Value

This function does not have any output, it just writes a SIF file, an edge attribute file, and a node attribute file

Note

The mapback of this function is still an open question, even in the Matlab version. Future developments will include more robust versions of the mapping back algorithm, probably as a separate mapback function.

Author(s)

M.K. Morris based on code by C. Terfve

See Also

writeNetwork

Examples

        data(ToyModel, package="CellNOptR")
        data(CNOlistToy,package="CellNOptR")
        paramsList = defaultParametersFuzzy(CNOlistToy, ToyModel)
        N = 10
        allRes = list()
 ## Not run: 
        for (i in 1:N){
            Res = CNORwrapFuzzy(CNOlistToy, ToyModel, paramsList)
            allRes[[i]] = Res
        }

        summary = compileMultiRes(allRes)
        summary$allFinalMSEs
        summary$allFinalNumParams
    
        writeFuzzyNetwork(postRefThresh, summary$allFinalMSEs, allRes)
    
## End(Not run)

saezlab/CNORfuzzy documentation built on May 3, 2019, 1:49 p.m.