diff options
Diffstat (limited to 'topics/systems')
| -rw-r--r-- | topics/systems/mariadb/precompute-mapping-input-data.gmi | 40 |
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? + |