inst/doc/subnet-sim.R

In LEANR: Finds "Local Subnetworks" Within an Interaction Network which Show Enrichment for Differentially Expressed Genes

## ---- eval=FALSE---------------------------------------------------------
#  library(LEANR)
#  library(ROCR)
#  set.seed(123456)
#  data(g2)

## ---- echo=FALSE,include=FALSE-------------------------------------------
library(LEANR)
library(ROCR)
set.seed(123456)
# load network and subnet results
instances<-LEANR:::instances
LEAN_results_sim<-LEANR:::LEAN_results_sim

## ---- eval=FALSE---------------------------------------------------------
#  n_instances=10
#  
#  instances<-lapply (1:n_instances,function(i){
#    subnet.simulation(g2, spec=sprintf('_STRING.fs900_rep%i',i), create.files=F)
#  })

## ---- eval=FALSE---------------------------------------------------------
#  LEAN_results_sim<-lapply(1:n_instances,function(i){
#    pvals<-instances[[i]]$pvals[,'P.Value']
#    names(pvals)<-rownames(instances[[i]]$pvals)
#    run.lean.fromdata(pvals, g2, n_reps = 1000, ncores = 3)
#  })

## ------------------------------------------------------------------------
# extract gene class labels for each of the simulation instances
gene.order<-rownames(instances[[1]]$pvals)
class_matrix<-t(foreach(i=1:length(instances),.combine=rbind) %do% {
  tmp<-!grepl('BG',instances[[i]]$pvals$NodeType);
  names(tmp)<-rownames(instances[[i]]$pvals);
  tmp[gene.order]
})

# extract LEAN scores for each of the simulation instances
LEAN_matrix<-t(foreach(i=1:length(instances),.combine=rbind) %do% {
  tmp<-LEAN_results_sim[[i]]$restab[,'pstar']
  names(tmp)<-rownames(LEAN_results_sim[[i]]$restab);
  tmp[gene.order]
})

# Extract single gene scores
SG_matrix<-t(foreach(i=1:length(instances),.combine=rbind) %do% {
  tmp<-instances[[i]]$pvals[,'P.Value']
  names(tmp)<-rownames(instances[[i]]$pvals);
  tmp[gene.order]
})

# ROC evaluation
predictions<-list(LEAN=prediction(-LEAN_matrix,class_matrix),
                  SG=prediction(-SG_matrix,class_matrix))

performances<-lapply(predictions,function(pred){performance(pred,"tpr","fpr")})
names(performances)<-names(predictions)

aucs_ind<-lapply(predictions,function(pred){performance(pred,"auc")@y.values})
aucs<-lapply(aucs_ind,function(x)mean(unlist(x)))
names(aucs)<-names(predictions)

## ---- fig.height=6, fig.width=6------------------------------------------
# plot resulting ROC curves
plot(performances$LEAN,xlim=c(0,.2),col='black',avg='vertical',lwd=3,
     spread.estimate='stderror',show.spread.at=seq(.02,.2,l=9),main='ROC performance on simulated subnetworks')
plot(performances$SG,col='orange',avg='vertical',lwd=3,add=T,
     spread.estimate='stderror',show.spread.at=seq(.02,.2,l=9))
abline(a=0,b=1,lty=2,col='cyan')
legend('topleft',c(sprintf('LEAN (AUC=%0.3g)',aucs$LEAN),sprintf('Single-gene (AUC=%0.3g)',aucs$SG)),fill=c('black','orange'))