Exercise 2: Solutions

#ex1
dat<-read.table("~/public/BIOL0021/networks.txt",header=T)
#ex2
dat[is.na(dat)]<-0.05
#ex3
cor(dat[,-c(1,2)])
cor(dat[,-c(1,2)],method="spearman")
#ex4
metanet<-apply(dat[,-c(1,2,7)],1,sum)
cor(metanet,dat[,7])
cor(metanet,dat[,7],method="spearman")
#ex5a
metanet>quantile(metanet,probs=0.95)->index
dat[index,c(1,2)]->top5
library(igraph)
graph_from_edgelist(as.matrix(top5))->top5g
#ex5b
neighbors(top5g,"FBgn0001180")->voisins
induced.subgraph(top5g,c(names(voisins),"FBgn0001180"))->sousg
plot(sousg, layout= layout.circle)
#ex5c
betweenness(top5g)->btw
evcent(top5g)$vector->ev
zscorebtw<-(btw-mean(btw))/sd(btw)
zscorebtw["FBgn0001180"]
zscoreev<-(ev-mean(ev))/sd(ev)
zscoreev["FBgn0001180"]
#ex5d (genes en aval)
neighbors(top5g,"FBgn0001180",mode="out")->index
which.min(zscoreev[index]+zscorebtw[index])