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authorPjotr Prins2024-04-17 03:15:17 -0500
committerPjotr Prins2024-04-17 03:15:17 -0500
commitdf169a3f64bf7bb944eab0013dee66e3ff95ad7f (patch)
tree242c226de3866c634703480027dbcdd750fe0c21 /issues/mgamma
parentc535013f8dad2b39cf8dadff61cea49e7ccef3c5 (diff)
downloadgn-gemtext-df169a3f64bf7bb944eab0013dee66e3ff95ad7f.tar.gz
mgamma: convert tasks
Diffstat (limited to 'issues/mgamma')
-rw-r--r--issues/mgamma/mgamma-convert.gmi12
1 files changed, 12 insertions, 0 deletions
diff --git a/issues/mgamma/mgamma-convert.gmi b/issues/mgamma/mgamma-convert.gmi
index d0ece51..bb19033 100644
--- a/issues/mgamma/mgamma-convert.gmi
+++ b/issues/mgamma/mgamma-convert.gmi
@@ -13,6 +13,18 @@ MGamma can convert between different formats.
* [ ] Store genotypes as floats instead of doubles in lmdb
* [ ] Add annotations to genotype lmdb format - probably as the first named columns
* [ ] Provide a metadata header in JSON that tracks such info and a version
+
+```
+{type: "geno", version:0.01, float: true, anno:["name","chr","pos"]}
+```
* [ ] Convert genotypes from strings using Rqtl2 CSV and metadata-JSON version of the control format, see
=> https://kbroman.org/qtl2/assets/vignettes/input_files.html
+
+* [ ] Write kinship lmdb as floats (half size)
+* [ ] If symmetric only store half the data
+* [ ] Add JSON meta header to track that information
+
+```
+{type: "GRM", version:0.01, float: true, symmetric: true}
+```