generatePACMENinput = function(Exprs,Mut,PPI=NULL,filename="PACMENinput.txt"){

  # last updated 29 October 2016
  # Exprs is a normalised gene expression matrix (can also be protein)
  ## Rows are genes and columns are samples
  # Mut is a mutation matrix, either binary (t-test), or non-negative score (linear regression) (can also be CNV)
  ## Rows are genes and columns are samples (columns must match with Exprs)
  ## You may want to preprocess Mut by removing genes with too few mutations before running this code
  ## by default this only considers genes with at least 3 non-zero entries, but you may want to filter this further.
  # PPI is network info as an adjacency matrix. If NULL then test all connections
  # filename to save tab-delimited results to, for uploading to PACMEN
  
  if (ncol(Exprs)!=ncol(Mut)) stop("Exprs and Mut must have same number of columns")
  if (is.null(PPI)) print("running with no interactome, testing all combinations...")
  
  require(limma)
  
  LMpairs = NULL
  
  #testableGenes = names(which(rowSums(Mut)>=3))
  testableGenes = names(which(apply(Mut,1,function(x) sum(x!=0)>=3)))
  if (!is.null(PPI)) {
  testableGenes = testableGenes[testableGenes %in% rownames(PPI)]
  }
  print(length(testableGenes))
    
  for (gene in testableGenes) {
    
    print(gene)
	if (!is.null(PPI)) {
	exprgenes = sort(c(gene,names(which(PPI[,gene]==1))))
    exprgenes = exprgenes[exprgenes %in% rownames(Exprs)]
	} else {
    exprgenes = rownames(Exprs)
	}
	if (length(exprgenes)==0) next
    ysmall = Exprs[exprgenes,,drop=FALSE]
	rownames(ysmall) <- exprgenes
    if (nrow(ysmall)==0) next
    design = model.matrix(~Mut[gene,])
    if (sum(design[,2])==0) next
    fit = lmFit(ysmall,design)
    fit = eBayes(fit)
    LMvalue = sign(fit$t[,2])
	LMp = fit$p.value[,2]
	
	#LMpairsShort = cbind(tail=gene,head=names(LMvalue),pval=LMp,dir=LMvalue)
	LMpairsShort = cbind(tail=gene,head=exprgenes,pval=LMp,dir=LMvalue)
	
	if (ncol(LMpairsShort)!=4) LMpairsShort=NULL
	
	LMpairs = rbind(LMpairs,LMpairsShort)
    
  }
  
  res = LMpairs
  rownames(res) <- NULL
  
  #if (!is.null(filename)) {
  print("saving data to file")
  write.table(res,file=filename,row.names=FALSE,col.names=TRUE,sep="\t",quote=FALSE)
  #}
  #return(res)
}