summaryrefslogtreecommitdiff
path: root/topics/systems/mariadb
diff options
context:
space:
mode:
authorPjotr Prins2023-12-10 08:12:19 -0600
committerPjotr Prins2023-12-10 08:13:48 -0600
commitd9e47731f8a1616b06fdc1ef2dbd3cf50413706d (patch)
tree96f8d9e5f7611b22e15c1d3e0160949757eb288d /topics/systems/mariadb
parent2fcee804ec2b5e409b7a623f0b154f275a14d5e1 (diff)
downloadgn-gemtext-d9e47731f8a1616b06fdc1ef2dbd3cf50413706d.tar.gz
Precompute notes on NAs
Diffstat (limited to 'topics/systems/mariadb')
-rw-r--r--topics/systems/mariadb/precompute-mapping-input-data.gmi22
1 files changed, 22 insertions, 0 deletions
diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi
index 12c21da..89bd8be 100644
--- a/topics/systems/mariadb/precompute-mapping-input-data.gmi
+++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi
@@ -979,6 +979,28 @@ Genotype state lives in 4 places. Time to create a 5th one with lmdb ;). At leas
Using this information we created our first phenotype file and GEMMA run!
+# Notes
+
+## NAs in GN
+
+A note from Zach:
+
+On Sat, Dec 09, 2023 at 06:09:56PM -0600, Zachary Sloan wrote:
+> (After typing the rest of this out, I realized that part of the
+> confusion might be about how locations are stored. We don't actually
+> database locations in the ProbeSetXRef table - we only database the
+> peak Locus marker name. This is then cross-referenced against the Geno
+> table, where the actual Location is stored. This is the main source of
+> the problem. So I think the best short-term solution might be to just
+> directly database the locations in the ProbeSetXRef table. Those
+> locations might become out of date, but as you mention they'd still
+> probably be in the same ballpark.)
+
+It is logical to store the location with the peak - if it changes we
+should recompute. That also adds the idea that we should track the
+version of the genotypes in that table.
+
+
## More complicated datasets
A good dataset to take apart is