From 51cde60bcc2f8a21c5caf3ab00f66967d17c2704 Mon Sep 17 00:00:00 2001
From: YangLabHKUST <66421162+YangLabHKUST@users.noreply.github.com>
Date: Mon, 8 Aug 2022 11:23:55 +0800
Subject: [PATCH] Update Format_data.R

---
 R/Format_data.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/Format_data.R b/R/Format_data.R
index a9c4ba6..59be1a7 100644
--- a/R/Format_data.R
+++ b/R/Format_data.R
@@ -240,6 +240,7 @@ format_data <- function(dat,
     # remove SNP with allele freqcy less than min_freq
     dat[is.na(dat$freq),"freq"] = 0.5
     dat = dat[dat$freq > min_freq & dat$freq < (1-min_freq), ]
+    message("Remove SNPs with MAF less than", min_freq, ", remaining ", nrow(dat), " SNPs.")
   }