R/deleteModOvlp.R

In bioinfoxh/term: Identification of Translational Efficiency Regulated Modules with ribosome profiling data

deleteModOvlp <- function(n_modules,networks,meetMin_cutoff){
  
  
  #library(Matrix);
  #lname=load("combine_nmodule(0.6_0.01).RData");
  
  moduleLen = sapply( n_modules, function(x) length(x$members) )
  n_modules = n_modules[order( moduleLen, decreasing=T )]
  
  
  num_module = 0;
  mname = c();
  
  num_network = dim(networks)[3]
  
  for(i in 1:length(n_modules)){
    
    temp.matrix = networks[n_modules[[i]]$members,n_modules[[i]]$members,];
    temp.unconnect = c();
    for(j in 1:num_network){
      temp.matrix1 = temp.matrix;
      diag(temp.matrix1[,,j]) = 0;
      temp.unconnect = c(which(rowSums(temp.matrix1)==0));
    }
    
    if(length(temp.unconnect)>0){
      temp.b = n_modules[[i]]$members;
      n_modules[[i]]$members = temp.b[-temp.unconnect];
    }
  }
  
  # for(i in 1:length(n_modules)){
  #  if (length(n_modules[[i]]$members)>=5){
  #     num_module=num_module+1;
  #     mname = c(mname,i);
  #     }
  # }
  #print("stop1 is okay");   # BREAK POINT1
  # delete = setdiff(c(1:length(n_modules)),mname);
  # #print(mname);
  # if (length(delete)>0){
  #   for (i in 1:length(delete)){
  #    n_modules[[delete[i]+1-i]]<-NULL;
  #   }
  # }
  
  #print(length(n_modules));
  #print("STOP2 is okay");   # BREAK POINT2
  
  #********************* remove the identical modules ************************
  
  #print(length(n_modules));
  
  start=1;
  index=1;
  while(index){
    tempcount = c();
    for(i in (start+1):length(n_modules)){
      temp1 = intersect(n_modules[[start]]$members,n_modules[[i]]$members);
      temp2 = n_modules[[i]]$members
      #temp2 = unique(union(n_modules[[start]]$members,n_modules[[i]]$members));
      if (length(temp1)>meetMin_cutoff*length(temp2)){
        tempcount=c(tempcount,i);
      }
    }
    if(length(tempcount)>0){
      n_modules[tempcount]<-NULL;
    }
    
    start=start+1;
    
    if(start<length(n_modules)){
      index=1;
    }else{
      index=0;
    }
  } 
  
  print(  paste( length(n_modules)," modules were detected after refinement",sep=""   ) );
  
  #***************************************************************************
  
  n_modules;
}