adjmatrix2edgelist: Convert network matrix to edge list

In wyguo/RLowPCor: Inference of co-expression gene network using relevance low order partial correlation from large scale expression data

Description

Convert the network matrix to edge list, in which the first column contains the regulators, the second column presents the target genes and edge weights are in the third column.

Usage

adjmatrix2edgelist(adjmatrix, cutoff = 0, directed = F, order = T)

Arguments

adjmatrix	a network matrix
cutoff	threshod to cut the edge weights. Only the edges that pass the threshold will be shown in the output results.
directed	logical, if FLASE the adjmatrix is transformed to symmetric matrix and the upper triangular part of the matrix is used to generate the edge list.
order	logical, to order the edgelist according the edge weightes or not.

Value

adjmatrix2edgelist returns a data frame of edge list.

Examples

##load data
library(RLowPC)
data(gnwdata)
data.exp<-gnwdata$size100$ts1[,-c(1:3)]
genes<-colnames(data.exp)
##build correlation network
inf.cor<-abs(cor(data.exp))
diag(inf.cor)<-0
##convert matrix to edge list
adjmatrix2edgelist(inf.cor)

wyguo/RLowPCor documentation built on May 4, 2019, 12:04 p.m.