R/linknum.arr.csum.R

In neaGUI: A user friendly R package to perform the network enrichment analysis (NEA).

linknum.arr.csum <-
function(ags, fgs, netlist2, gnum=TRUE, gsym)
{
  if(!is.list(fgs)) fgs = list(fgs)
  nfgs<-length(fgs)

## numbered version
  g123= 1:length(gsym)
  names(g123)= gsym

## translate ags and fgs into numbers
  agsnum = g123[ags]
    agsnum= agsnum[!is.na(agsnum)]

## output
  nlink<- matrix(0, nrow=nfgs, ncol=length(agsnum))
    rownames(nlink)<-names(fgs)
  
## sub-network
for (i in 1:nfgs){
  fgsnum= g123[fgs[[i]]]  ## numbered version of fgs
  num = as.character(unique(c(agsnum, fgsnum)))

## sub-network1: col1 as index
  netlist= netlist2$list1
  sub = num[num %in% names(netlist)]
  subnet = netlist[sub]

## expand sub-network to a vector form
    nnet = sapply(subnet, length)
    gg1 = rep(sub, nnet)
    gg2 = unlist(subnet)
    asubnet1 = paste(gg1, gg2) ## 1-2 direction here

## sub-network2: col2 as index
  netlist= netlist2$list2
  sub = num[num %in% names(netlist)]
  subnet = netlist[sub]

## expand sub-network to a vector form
    nnet = sapply(subnet, length)
    gg1 = rep(sub, nnet)
    gg2 = unlist(subnet)
    asubnet2 = paste(gg2, gg1)  ## note the 2-1 direction here!!
                                ## may contain mirror images of the first subnet
     asubnet2rv = paste(gg1, gg2) 
    mirror = asubnet2rv %in% asubnet1
## 
    asubnet = c(asubnet1, asubnet2[!mirror])  # no mirror images   

## count links on sub-network
    agsfgs<- matrix(outer(agsnum,fgsnum,paste), ncol=length(fgsnum))
    fgsags<- t(matrix(outer(fgsnum,agsnum,paste), ncol=length(agsnum)))
    ugsnum<-cbind(agsfgs,fgsags) ### we do not need to use "unique" function
    a = matrix(ugsnum %in% asubnet, ncol=ncol(ugsnum))
    nlink[i,]<- cumsum(rowSums(a))
}
return(nlink)
}