"CpermSigMeta.MBparams.MBnetwork.MBdataDE.MBgibbsPars" <-
function(params,graph,data,gibbsPars,quiet=FALSE,lib="YEAST",what=c("BP","MF","CC","KEGG"),universe=NULL,num="data",pcut=.05,nperm=100,contrasts=NULL,...)
{
# Compatibility checks
    isCompat1 <- compatObjects(params,graph)
    isCompat2 <- compatObjects(graph,data)
    isValid <- validObject(gibbsPars)

    if((num != "data") && (!is.numeric(num) || (as.integer(num) != num) || (num <= 0) || (num > data@N)))
      stop("Invalid num specification")
    if(num == "data") num <- floor(data@prop*data@N)
    what <- match.arg(what)

# Run Gibbs sampler on all data
    if(!quiet) cat("\nRunning gibbs sampler and term finder on all data...\n\n")
    graph <- calcCPDs(x=graph,data=data,contrasts)
    graph <- CgibbsSampler(x=graph,params=params,gibbsPars=gibbsPars,quiet=quiet,...)

# Perform meta-data Term Finder on orig. data
    tempTF <- GOKEGGHyperG(data@IDs[which(rank(-1*calcLods(graph)) <= num)],lib=lib,what=what,universe=universe)
    pval.orig <- tempTF$pvalues[order(names(tempTF$pvalues))]

# Save old cpds
    cpds.old <- graph@Cpds
    
# Run permutation gibbs sampler and meta-data Term Finder
    pval.rand <- matrix(nrow=length(pval.orig),ncol=nperm)
    for(i in 1:nperm) {
      if(!quiet) cat(paste("\nRunning gibbs sampler and term finder on permutation ",i,"...\n\n",sep=""))
      graph@Cpds <- graph@Cpds[,sample(1:graph@N)]
      graph <- CgibbsSampler(x=graph,params=params,gibbsPars=gibbsPars,quiet=quiet,...)
      tempTF <- GOKEGGHyperG(data@IDs[which(rank(-1*calcLods(graph)) <= num)],lib=lib,what=what,universe=universe)
      pval.rand[,i] <- tempTF$pvalues[order(names(tempTF$pvalues))]
      graph@Cpds <- cpds.old
    }

# Calculate permutation significance
    pval.perm <- apply(cbind(pval.orig,pval.rand),1,function(x) sum(x[2:(nperm+1)][!is.na(x[2:(nperm+1)])] <= x[1])/sum(!is.na(x[2:(nperm+1)])))
    nsig <- sum(pval.perm <= pcut,na.rm=TRUE)

    return(nsig)
}