diff options
Diffstat (limited to 'topics')
| -rw-r--r-- | topics/gn1-migration-to-gn2/clustering.gmi | 20 |
1 files changed, 18 insertions, 2 deletions
diff --git a/topics/gn1-migration-to-gn2/clustering.gmi b/topics/gn1-migration-to-gn2/clustering.gmi index 186228f..08b3686 100644 --- a/topics/gn1-migration-to-gn2/clustering.gmi +++ b/topics/gn1-migration-to-gn2/clustering.gmi @@ -200,12 +200,28 @@ For the actual heatmap representation, it looks to me like the `neworder` variab is what is populated and used to draw the "cells" of the heatmap diagram: see -=> https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L206-L316 +=> https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L206-L316 this chunk. -This has not yet been migrated over +This has not yet been migrated over. + +Within the loop that uses `neworder`, there is a call to `genotype.regression(...)` function. + +From what I (fredmanglis) can tell, it seems this `regression` function might be the one defined in the + +=> https://github.com/genenetwork/QTLReaper/blob/master/Src/dataset.c#L416 QTLReaper library. + +I am not entirely sure where we stand on the use of QTLReaper. I think there was a move away from using this library some time in the past. There **might** be need to migrate the => https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/heatmap/Heatmap.py#L419-L438 `getNearestMarker` function out So, it does seem like I had previously missed out on a lot of extra computation that still needs migration. + +### 2021-08-20 14:15 + +The `neworder` variable setup has been partially migrated. The use of the `xoffset` and `d_1` variables has not been cleared up at this point - they could be removed in the future. + +Also migrated retrieval of strains with non-NoneType values + +Awaiting response on use of QTLReaper. |