diff options
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/gemma/lmm-precomputed-scores.gmi | 37 | ||||
| -rw-r--r-- | issues/strainid-wrong-for-bxd.gmi | 56 |
2 files changed, 64 insertions, 29 deletions
diff --git a/issues/gemma/lmm-precomputed-scores.gmi b/issues/gemma/lmm-precomputed-scores.gmi index 744d51a..8db9722 100644 --- a/issues/gemma/lmm-precomputed-scores.gmi +++ b/issues/gemma/lmm-precomputed-scores.gmi @@ -7,36 +7,15 @@ Here we will track introducing a new precomputation of scores for GN. Interestin * assigned: pjotrp * priority: high * type: bug, enhancement -* status: unclear +* status: ongoing * 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 (?) - -Moved to +# Tasks -=> ../../topics/systems/mariadb/precompute-mapping-input-data.gmi +* [ ] Add the log values, effect size and number of individuals to the xapian search. + +# Note -* closed +First implementation in + +=> ../../topics/systems/mariadb/precompute-mapping-input-data.gmi diff --git a/issues/strainid-wrong-for-bxd.gmi b/issues/strainid-wrong-for-bxd.gmi new file mode 100644 index 0000000..21bd2d8 --- /dev/null +++ b/issues/strainid-wrong-for-bxd.gmi @@ -0,0 +1,56 @@ +# StrainId wrong + +# Tags +* assigned: arthurc +* type: bug +* status: unknown + +# Info + +When I do: + +``` +MariaDB [db_webqtl]> SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = 1; +``` + +I get a list of BXDs (good), but also + +``` +| 333 | BXH2 | +| 334 | BXH3 | +| 336 | BXH5 | +| 342 | BXH11 | +| 343 | BXH12 | +| 43879 | BXH12a | +| 43880 | BXH13 | +| 43881 | HXB1 | +| 43882 | HXB2 | +| 43883 | HXB3 | +| 43884 | HXB4 | +``` + +This is probably wrong? + + +``` +MariaDB [db_webqtl]> select * from InbredSet where InbredSetId=1 limit 3; ++----+-------------+---------------+------+-----------+------------+--------+-----------------+-------------+--------------------------------- +-----------------+-------------+-------------+---------------+ +| Id | InbredSetId | InbredSetName | Name | SpeciesId | FullName | public | MappingMethodId | GeneticType | Family + | FamilyOrder | MenuOrderId | InbredSetCode | ++----+-------------+---------------+------+-----------+------------+--------+-----------------+-------------+--------------------------------- +-----------------+-------------+-------------+---------------+ +| 1 | 1 | BXD | BXD | 1 | BXD Family | 2 | 1 | riset | Reference Populations (replicate + average, SE, N) | 1 | 0 | BXD | ++----+-------------+---------------+------+-----------+------------+--------+-----------------+-------------+--------------------------------- +-----------------+-------------+-------------+---------------+ + +MariaDB [db_webqtl]> select * from StrainXRef where InbredSetId=1 and StrainID=43889 limit 3; ++-------------+----------+---------+------------------+----------------+ +| InbredSetId | StrainId | OrderId | Used_for_mapping | PedigreeStatus | ++-------------+----------+---------+------------------+----------------+ +| 1 | 43889 | 1247 | N | NULL | ++-------------+----------+---------+------------------+----------------+ +``` + +Not a BXD. Not even a mouse. |