R/ganet.ComLinks.R

In altayg/ganet: Global Assessment of NETwork Inference Algorithms Based on the Available Literature of Gene/Protein Interactions

ganet.ComLinks <- function(netlist, netdata, uppercase=FALSE)
{#assumes the first and second columns have genes for interaction
  #e.g. assume netdata is a interaction database
  #netlist is the prediction set
  if(uppercase){
    netlist <-as.matrix(netlist)
    netlist[,1] <- toupper(as.character(netlist[,1]))
    netlist[,2] <- toupper(as.character(netlist[,2]))
    netdata <-as.matrix(netdata)
    netdata[,1] <- toupper(as.character(netdata[,1]))
    netdata[,2] <- toupper(as.character(netdata[,2]))    
  }else{
  netlist <-as.matrix(netlist)
  netdata <- as.matrix(netdata)
  }
  #
  a <- paste(netlist[,1],netlist[,2])
  b <- paste(netlist[,2],netlist[,1])
  
  x<- paste(netdata[,1], netdata[,2])
  
  i1<- which(a %in% x)
  i2<- which(b %in% x)
  ind <- union(i1,i2)
  res <- cbind(netlist[ind,],ind)
  return(res)
}