summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorPjotr Prins2023-03-24 07:15:22 +0100
committerPjotr Prins2023-03-24 07:15:22 +0100
commit03f29b98d4b7468b63cf6fd0cc6cc6abfd558b3d (patch)
tree1433251b38ccd534afff62267965a4f2d56850d0
parent0c679f8f62f769b380f4d407cbf3cc087cfec86a (diff)
downloadgn-gemtext-03f29b98d4b7468b63cf6fd0cc6cc6abfd558b3d.tar.gz
ProbeSetXRef
-rw-r--r--topics/systems/mariadb/precompute-mapping-input-data.gmi40
1 files changed, 39 insertions, 1 deletions
diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi
index 733faea..9ce4c95 100644
--- a/topics/systems/mariadb/precompute-mapping-input-data.gmi
+++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi
@@ -113,4 +113,42 @@ From this exercise we can conclude:
Rob voiced a wish to retain all scores (at least those above 1.0). This is not feasible in mariadb, but we can retain GEMMA output if stored efficiently.
-ProbeSetXRef is pretty small, currently @5.6Gb and 48,307,650 rows, so we could decide to add columns to track different mappers.
+## Notes on ProbeSetXRef
+
+ProbeSetXRef is pretty small, currently @5.6Gb and 48,307,650 rows, so we could decide to add columns to track different mappers. Something funny
+
+```
+select count(LRS) from ProbeSetXRef;
++------------+
+| count(LRS) |
++------------+
+| 28335955 |
++------------+
+```
+
+half the fields are used. What to think of
+
+```
+MariaDB [db_webqtl]> select * from ProbeSetXRef where LRS=0 limit 5;
++------------------+------------+----------+-----------+---------+------------+------+------+----------------+------+--------+----------+------+
+| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old | LRS_old | pValue_old | mean | se | Locus | LRS | pValue | additive | h2 |
++------------------+------------+----------+-----------+---------+------------+------+------+----------------+------+--------+----------+------+
+| 589 | 8599010 | 70606737 | NULL | NULL | NULL | 0 | NULL | rsm10000000001 | 0 | NULL | 0 | NULL |
+| 589 | 8593710 | 70606738 | NULL | NULL | NULL | 0 | NULL | rsm10000000001 | 0 | NULL | 0 | NULL |
+| 589 | 8607637 | 70606739 | NULL | NULL | NULL | 0 | NULL | rsm10000000001 | 0 | NULL | 0 | NULL |
+| 589 | 8594490 | 70606740 | NULL | NULL | NULL | 0 | NULL | rsm10000000001 | 0 | NULL | 0 | NULL |
+| 589 | 8591994 | 70606741 | NULL | NULL | NULL | 0 | NULL | rsm10000000001 | 0 | NULL | 0 | NULL |
++------------------+------------+----------+-----------+---------+------------+------+------+----------------+------+--------+----------+------+
+```
+
+```
+MariaDB [db_webqtl]> select count(*) from ProbeSetXRef where LRS=0 and Locus="rsm10000000001";
++----------+
+| count(*) |
++----------+
+| 291447 |
++----------+
+```
+
+There is obviously more. I think this table can use some cleaning up?
+