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| author | Alexander_Kabui | 2025-09-04 17:47:33 +0300 |
|---|---|---|
| committer | Pjotr Prins | 2026-01-05 11:12:10 +0100 |
| commit | 0c241d7ced63fa8ef15895a7aa99ff740ede63d3 (patch) | |
| tree | e44f4bdc99f6f59a48ceaf592a91473de9c089bf | |
| parent | 4c11fa12c67091b56299a90c707d0a0af419ea27 (diff) | |
| download | gn-gemtext-0c241d7ced63fa8ef15895a7aa99ff740ede63d3.tar.gz | |
feat: Update rqtl2 lmdb notes.
| -rw-r--r-- | topics/lmms/rqtl2/using-rqtl2-lmdb-adapter.gmi | 17 |
1 files changed, 17 insertions, 0 deletions
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 |