tests/Examples/diffnet_ex.R

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

############################################################
##This example illustrates the use of Differential Network##
############################################################


##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 null hypothesis (both datasets have the same underlying
## network)
library('mvtnorm')
x1 <- rmvnorm(n,mean = rep(0,p), sigma = cor1)
x2 <- rmvnorm(n,mean = rep(0,p), sigma = cor1)

##run diffnet (under null hypothesis)
dn.null <- diffnet_multisplit(x1,x2,b.splits=1,verbose=FALSE)
dn.null$ss.pval#single-split p-value

##generate data under alternative hypothesis (datasets have different networks)
x1 <- rmvnorm(n,mean = rep(0,p), sigma = cor1)
x2 <- rmvnorm(n,mean = rep(0,p), sigma = cor2)

##run diffnet (under alternative hypothesis)
dn.altn <- diffnet_multisplit(x1,x2,b.splits=1,verbose=FALSE)
dn.altn$ss.pval#single-split p-value
dn.altn$medagg.pval#median aggregated p-value

##typically we would choose a larger number of splits
# dn.altn <- diffnet_multisplit(x1,x2,b.splits=10,verbose=FALSE)
# dn.altn$ms.pval#multi-split p-values
# dn.altn$medagg.pval#median aggregated p-value
# plot(dn.altn)#histogram of single-split p-values