From 71a4fb1dacc5c68c42694907a218f6f763f29762 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 16 Mar 2023 12:08:59 +0100
Subject: Starting on gemma precompute

---
 issues/gemma/lmm-precomputed-scores.gmi | 36 +++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)
 create mode 100644 issues/gemma/lmm-precomputed-scores.gmi

(limited to 'issues/gemma/lmm-precomputed-scores.gmi')

diff --git a/issues/gemma/lmm-precomputed-scores.gmi b/issues/gemma/lmm-precomputed-scores.gmi
new file mode 100644
index 0000000..1a86e12
--- /dev/null
+++ b/issues/gemma/lmm-precomputed-scores.gmi
@@ -0,0 +1,36 @@
+# LMM precomputed scores
+
+Here we will track introducing a new precomputation of scores for GN. Interestingly, this ties in with our xapian search and fast querying of value ranges.
+
+# Tags
+
+* assigned: pjotrp
+* priority: high
+* type: bug, enhancement
+* status: unclear
+* keywords: database, gemma, reaper
+
+# Old storage
+
+The old reaper scores are in
+
+```
+MariaDB [db_webqtl]> select ProbeSetId,ProbeSetFreezeId,Locus,LRS,additive from ProbeSetXRef limit 10;
++------------+------------------+----------------+------------------+--------------------+
+| ProbeSetId | ProbeSetFreezeId | Locus          | LRS              | additive           |
++------------+------------------+----------------+------------------+--------------------+
+|          1 |                1 | rs13480619     |  12.590069931048 |        -0.28515625 |
+|          2 |                1 | rs29535974     | 10.5970737900941 | -0.116783333333333 |
+|          3 |                1 | rs49742109     |  6.0970532702754 |  0.112957489878542 |
+|          4 |                1 | rsm10000002321 | 11.7748675511731 | -0.157113725490196 |
+|          5 |                1 | rsm10000019445 | 10.9232633740162 |  0.114764705882353 |
+|          6 |                1 | rsm10000017255 | 8.45741703245224 | -0.200034412955466 |
+|          7 |                1 | rs4178505      | 7.46477918183565 |  0.104331983805668 |
+|          8 |                1 | rsm10000144086 | 12.1201771258006 | -0.134278431372548 |
+|          9 |                1 | rsm10000014965 | 11.8837168740735 |  0.341458333333334 |
+|         10 |                1 | rsm10000020208 | 10.2809848009836 | -0.173866666666667 |
++------------+------------------+----------------+------------------+--------------------+
+10 rows in set (0.000 sec)
+```
+
+This means for every dataset one single maximum score gets stored (?)
-- 
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