pred.network {BUS} | R Documentation |
To predict the matrix of gene network, based on the similarity matrix and filtered according to a corrected p-value matrix.
pred.network(pM,similarity,thresh)
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. |
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).
Yin Jin, Hesen Peng, Lei Wang, Raffaele Fronza, Yuanhua Liu and Christine Nardini
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)