Making edge lists for correlation networks

correlation edge list

#------------------------------------------------------
# demonstration of making edge lists for 
# correlation network analysis 
# by Dmitry Grapov
# 031814
#------------------------------------------------------

# load devium library for all functions
source("http://pastebin.com/raw.php?i=JVyTrYRD") # sources function to download github repo (https://github.com/dgrapov/devium)

#example data
data(mtcars)
tmp.data<-mtcars # change column names to numeric index for a more robust key, this key will need to match variable properties in the node attributes file

#calculate correlation based edge list
correl<-devium.calculate.correlations(tmp.data,type="spearman", results = "edge list")
correl$fdr.p<-p.adjust(correl$p.values, method = "BH", n = length(correl$p.values)) # FDR adjusted p-values


#(optional) limit maximum number of connections (max.edges) per source node
# fxn allows more than max.edges to connect otherwise disconnected nodes 
filtered.id<-edge.list.filter.partial(edge.list=correl[,1:2],weight=correl[,3],max.edges=5)
correl<-correl[filtered.id,]


#prepare for network mapping
edge.list<-correl[,1:2]
edge.list$color<-"positive"
edge.list$color[correl$value<0]<-"negative"
edge.list$width<-abs(correl$value)

#filter based on p<0.05 
edge.list<-edge.list[correl$p.values<0.05,] # change optionally to correl$fdr.p for FDR adjusted correlations (could use package FDRtools for more robust measure)


write.csv(edge.list,file="edge list.csv",row.names = FALSE) # save as CSV