diff --git a/vignettes/cepo.Rmd b/vignettes/cepo.Rmd index 935ae07..408a595 100644 --- a/vignettes/cepo.Rmd +++ b/vignettes/cepo.Rmd @@ -290,8 +290,10 @@ 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$stats) fgseaRes <- fgsea(pathways = hallmarkList, - stats = sort(as.data.frame(ds_res_batches$average$stats)$beta), + stats = sort(stats), minSize = 15, maxSize = 500)