pred.network {BUS} | R Documentation

## Predict the network

### Description

To predict the matrix of gene network, based on the similarity matrix and filtered according to a corrected p-value matrix.

### Usage

    pred.network(pM,similarity,thresh)

### Arguments

`pM` | A corrected p-value matrix, a MxM matrix for significance of similarity among M genes.
`similarity` | A MxM matrix for similarity between genes.
`thresh` | Threshold for significance of the p-value.

### Value

A MxM matrix of the predicted network, where cell emphij infers a link between gene i and j and set 0 when the p-value is not significant (no link).

### Author(s)

Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini

### Examples

    data(copasi)
    mat<-as.matrix(copasi[1:10,])
    rownames(mat)<-paste("G",1:nrow(mat), sep="")
    similarity=gene.similarity(mat,measure="MI",net.trim="mrnet")
    pM=gene.pvalue(mat,measure="MI",net.trim="mrnet")$single.perm.p.value
    pred.network(pM,similarity,thresh=0.05)

[Package BUS version 1.44.0 Index]