From 2bd7b74814ca208a30382c6ad847e169addc542d Mon Sep 17 00:00:00 2001
From: Arun Isaac
Date: Thu, 13 Nov 2025 02:23:34 +0000
Subject: Add JWAS tests to HSmice test.

---
 e2e-tests/hsmice/jwas-manhattan.r | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 e2e-tests/hsmice/jwas-manhattan.r

(limited to 'e2e-tests/hsmice/jwas-manhattan.r')

diff --git a/e2e-tests/hsmice/jwas-manhattan.r b/e2e-tests/hsmice/jwas-manhattan.r
new file mode 100644
index 0000000..a437a8c
--- /dev/null
+++ b/e2e-tests/hsmice/jwas-manhattan.r
@@ -0,0 +1,13 @@
+library(dplyr)
+library(qqman)
+library(readr)
+
+args = commandArgs(trailingOnly=TRUE)
+if (length(args) != 1) {
+    write("Usage: Rscript jwas-manhattan.r GWAS-FILE", stderr())
+    quit(status=1)
+}
+gwas_file = args[1]
+
+gwas = mutate(read_tsv(gwas_file), antilog=10^(-modelfrequency))
+manhattan(gwas, chr="chromosome", bp="position", snp="marker_ID", p="antilog")
-- 
cgit 1.4.1