BUS (version 1.28.0)

pred.network: 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).

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)