From 0c241d7ced63fa8ef15895a7aa99ff740ede63d3 Mon Sep 17 00:00:00 2001
From: Alexander_Kabui
Date: Thu, 4 Sep 2025 17:47:33 +0300
Subject: feat: Update rqtl2 lmdb notes.

---
 topics/lmms/rqtl2/using-rqtl2-lmdb-adapter.gmi | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

(limited to 'topics/lmms')

diff --git a/topics/lmms/rqtl2/using-rqtl2-lmdb-adapter.gmi b/topics/lmms/rqtl2/using-rqtl2-lmdb-adapter.gmi
index 2fa0491..bea482d 100644
--- a/topics/lmms/rqtl2/using-rqtl2-lmdb-adapter.gmi
+++ b/topics/lmms/rqtl2/using-rqtl2-lmdb-adapter.gmi
@@ -60,7 +60,24 @@ guix shell r r-thor r-rjson r-qtl2 -- \
 
 # Example
 Rscript https://github.com/genenetwork/genenetwork3/pull/235/files ./lmdb_path
+
+
 ```
+### using this with rqtl2 Example
+
+```r
+cross <- read_lmdb_cross(LMDB_DB_PATH)
+summary(cross)
+cat("Is this cross okay", check_cross2(cross), "\n")
+warnings() #  enable warnings for the debug purposes  only!
+pr <- calc_genoprob(cross)
+out <- scan1(pr, cross$pheno, cores=4)
+par(mar=c(5.1, 4.1, 1.1, 1.1))
+ymx <- maxlod(out)
+plot(out, cross$gmap, lodcolumn=1, col="slateblue") # test generating of qtl plots
+
+```
+
 
 ### References
 => https://kbroman.org/qtl2/assets/vignettes/developer_guide.html
-- 
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