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| author | Pjotr Prins | 2024-09-02 14:05:05 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2024-09-02 14:05:05 +0200 |
| commit | d35332d6d6fc5155f9c904bb9a8a23ee4787abe5 (patch) | |
| tree | c92adc06726919211f186aa0ea8eb831d819e8df /topics/lmms/gemma | |
| parent | b9f5da8ba86ef48eccb5f7f75c718cae87a91e44 (diff) | |
| download | gn-gemtext-d35332d6d6fc5155f9c904bb9a8a23ee4787abe5.tar.gz | |
Permutations: dealing with phenotypes
Diffstat (limited to 'topics/lmms/gemma')
| -rw-r--r-- | topics/lmms/gemma/permutations.gmi | 8 |
1 files changed, 6 insertions, 2 deletions
diff --git a/topics/lmms/gemma/permutations.gmi b/topics/lmms/gemma/permutations.gmi index c0a930e..6715435 100644 --- a/topics/lmms/gemma/permutations.gmi +++ b/topics/lmms/gemma/permutations.gmi @@ -411,14 +411,14 @@ Now I have to deal with phenotype files as they are rewritten. We should still c Note that we can use -p if --phenotypes is NOT defined. Problem is we have a few paths now: * [X] Check phenotypes are directly passed into GEMMA with -p switch -* [ ] Check phenotypes are passed in as a file +* [ ] Check phenotypes are passed in as a file with --phenotypes switch * [ ] Check phenotypes are coming in using the JSON file Fixed the first one with => https://github.com/genetics-statistics/gemma-wrapper/commit/2b7570a7f0ba0d1080c730b208823c0622dd8f2c -though that does not do caching (yet). +though that does not do caching (yet). Next stop doing LOCO I notice xz is phenomenally slow. Turns out it was not xz, but when using `tar -C` we switch into the path and somehow xz kept growing its output. ## Dealing with epoch @@ -431,3 +431,7 @@ We have two or more possible solutions to deal with hierarchy in the population. ## Covariates * [ ] Try covariates Dave + +## Later + +* [ ] Fix running of -p switch when assoc cache exists (bug) |