"CpriorEnrich.MBparams.MBnetwork.MBdataDE.MBgibbsPars" <- function(params,graph,data,gibbsPars,quiet=FALSE,prior.genes,contrasts=NULL,...) { # Compatibility checks isCompat1 <- compatObjects(params,graph) isCompat2 <- compatObjects(graph,data) isValid <- validObject(gibbsPars) # Run Gibbs sampler if(!quiet) cat("\nRunning gibbs sampler...\n\n") graph <- calcCPDs(x=graph,data=data,contrasts) graph <- CgibbsSampler(x=graph,params=params,gibbsPars=gibbsPars,quiet=quiet,...) scores <- calcLods(graph) # Enrichment analysis if(!quiet) cat("\nCalculating enrichment of known DE genes...\n\n") #scores[is.na(scores)] <- min(scores,na.rm=TRUE)-1 enrich <- ks.test(scores[graph@Names %in% prior.genes],scores[!(graph@Names %in% prior.genes)],alternative="less")$statistic return(enrich) }