Correction for the case of enpty enrichment results.

enrichment/enrich_maps.R

@@ -112,14 +112,18 @@ library(enrichR)
 
 message("Enrichment of pathways")
 
+### Header of the enrichment table, it's consecutive segments will be written
+### later below
 cat(file = "enriched_pathways.txt", 
     "pathway_db\tTerm\tAdjusted.P.value\n",
     append = F)
 
 pathway_dbs <- config[config$type == "pathway_db","resource"]
 
+### Run Enrichr
 enriched_pathways <- enrichr(input, databases = pathway_dbs)
 
+### Leave only the pathways with adjusted p lower than 0.1 
 adj_pathways <- lapply(enriched_pathways, 
                        function(x) {
                           selected <- which(x$Adjusted.P.value < 0.1)
@@ -129,8 +133,12 @@ adj_pathways <- lapply(enriched_pathways,
                           x[selected, ]
                         })
 
-for(aep in 1:length(adj_pathways)) {
-  write.table(cbind(pathway_db = pathway_dbs[aep], 
+### Clean empty results
+adj_pathways <- adj_pathways[sapply(adj_pathways, dim)[1,] > 0]
+
+### Write results down in the file
+for(aep in names(adj_pathways)) {
+  write.table(cbind(pathway_db = aep, 
                     adj_pathways[[aep]][,c("Term","Adjusted.P.value")], 
                     stringsAsFactors = F), 
               file = "enriched_pathways.txt", sep = "\t", quote = F, col.names = F, row.names = F, append = T)