bioc check

Author: HaniJieunKim

vignettes/cepo.Rmd

@@ -290,10 +290,8 @@ library(fgsea)
 hallmarkList <- getGeneSets(species = "Homo sapiens", 
                            library = "H")
 
-stats = as.data.frame(ds_res_batches$average$stats)$beta
-names(stats) = rownames(ds_res_batches$average$stats)
 fgseaRes <- fgsea(pathways = hallmarkList, 
-                  stats    = sort(stats),
+                  stats    = sort(ds_res_batches[4]$average$stats[,"beta"]),
                   minSize = 15,
                   maxSize = 500)