moduleIdentificationGPFixSSMultilayer {AMOUNTAIN} | R Documentation

## Module Identification for multi-layer network

### Description

Algorithm for Module Identification on multi-layer network sharing the same set of genes

### Usage

    moduleIdentificationGPFixSSMultilayer(W, listz, x0, a = 0.5, lambda = 1,
      maxiter = 1000)

### Arguments

`W` | edge score matrix of the network, n x n matrix
`listz` | a list of node score vectors, each layer has a n-length vector
`x0` | initial solution, n-length vector
`a` | parameter in elastic net the same as in `EuclideanProjectionENNORM`
`lambda` | parameter in objective, coefficient of node score of other layers
`maxiter` | maximal interation of whole procedure

### Value

a list containing objective values and solution

### Author(s)

Dong Li, dxl466@cs.bham.ac.uk

### References

AMOUNTAIN

### See Also

`moduleIdentificationGPFixSSMultilayer`

### Examples

    n = 100
    k = 20
    L = 5
    theta = 0.5
    cpl <- multilayernetworkSimulation(n,k,theta,L)
    listz <- list()
    for (i in 1:L){
    listz[[i]] <- cpl[[i+2]]
    }
    moduleid <- cpl[[2]]
    ## use default parameters here
    x <- moduleIdentificationGPFixSSMultilayer(cpl[[1]],listz,rep(1/n,n))
    predictedid <- which(x[[2]]!=0)
    recall <- length(intersect(predictedid,moduleid))/length(moduleid)
    precise <- length(intersect(predictedid,moduleid))/length(predictedid)
    Fscore <- (2*precise*recall/(precise+recall))

[Package AMOUNTAIN version 1.8.0 Index]