From c277e0fba734bea963b467cb21684a261ba8d5c3 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Wed, 8 Apr 2026 08:57:35 -0500
Subject: [PATCH] Update sumstats_qc.R

---
 R/sumstats_qc.R | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/R/sumstats_qc.R b/R/sumstats_qc.R
index 2200634e..1c000998 100644
--- a/R/sumstats_qc.R
+++ b/R/sumstats_qc.R
@@ -26,10 +26,18 @@ rss_basic_qc <- function(sumstats, LD_data, skip_region = NULL, keep_indel = TRU
     stop("Missing columns in sumstats: ", paste(missing_cols, collapse = ", "))
   }
 
+  # Dynamically detect which effect columns exist to flip
+  # Must have at least one of beta or z
+  flip_candidates <- c("beta", "z")
+  col_to_flip <- intersect(flip_candidates, colnames(sumstats))
+  if (length(col_to_flip) == 0) {
+    stop("sumstats must contain at least one of: 'beta', 'z'")
+  }
+
   ref_variants <- LD_data$LD_variants
 
   allele_flip <- allele_qc(sumstats, ref_variants,
-    col_to_flip = c("beta", "z"),
+    col_to_flip = col_to_flip,
     match_min_prop = 0, remove_dups = TRUE, remove_indels = !keep_indel,
     remove_strand_ambiguous = TRUE
   )