tests/Examples/diffnet_ss_ex.R

In FrankD/nethet: A bioconductor package for high-dimensional exploration of biological network heterogeneity

##set seed
set.seed(1)

##sample size and number of nodes
n <- 40
p <- 10

##specifiy sparse inverse covariance matrices
gen.net <- generate_2networks(p,graph='random',n.nz=rep(p,2),
                              n.nz.common=ceiling(p*0.8))
invcov1 <- gen.net[[1]]
invcov2 <- gen.net[[2]]
plot_2networks(invcov1,invcov2,label.pos=0,label.cex=0.7)

##get corresponding correlation matrices
cor1 <- cov2cor(solve(invcov1))
cor2 <- cov2cor(solve(invcov2))

##generate data under alternative hypothesis
library('mvtnorm')
x1 <- rmvnorm(n,mean = rep(0,p), sigma = cor1)
x2 <- rmvnorm(n,mean = rep(0,p), sigma = cor2)

##run diffnet
split1 <- sample(1:n,20)#samples for screening (condition 1)
split2 <- sample(1:n,20)#samples for screening (condition 2)
dn <- diffnet_singlesplit(x1,x2,split1,split2)
dn$pval.onesided#p-value