removed lower, upper variables from return in do_gsea_pod

rela-v · rela-v · commit 4894e66282e3 · 2025-11-04T10:24:59.000-05:00
diff --git a/R/do_gsea_pod.R b/R/do_gsea_pod.R
@@ -72,7 +72,7 @@ do_gsea_pod <- function(bpn, species = "hsapiens", gmtfile = NULL,
   results <- fgsea::fgsea(pathways, ranked, minSize = minSize, maxSize = maxSize)
 
   g <- GSEAResult(
-    results, pathways, lower, upper, alpha, upreg, downreg, useFDR
+    results, pathways, alpha, upreg, downreg, useFDR
   )
 
   gsea(bpn) <- g

Original file line number	Diff line number	Diff line change
`@@ -72,7 +72,7 @@ do_gsea_pod <- function(bpn, species = "hsapiens", gmtfile = NULL,`
`72`	`72`	`results <- fgsea::fgsea(pathways, ranked, minSize = minSize, maxSize = maxSize)`
`73`	`73`
`74`	`74`	`g <- GSEAResult(`
`75`		`- results, pathways, lower, upper, alpha, upreg, downreg, useFDR`
	`75`	`+ results, pathways, alpha, upreg, downreg, useFDR`
`76`	`76`	`)`
`77`	`77`
`78`	`78`	`gsea(bpn) <- g`