diff options
Diffstat (limited to 'topics/lmms')
| -rw-r--r-- | topics/lmms/gemma/permutations.gmi | 17 |
1 files changed, 16 insertions, 1 deletions
diff --git a/topics/lmms/gemma/permutations.gmi b/topics/lmms/gemma/permutations.gmi index 7327227..6715435 100644 --- a/topics/lmms/gemma/permutations.gmi +++ b/topics/lmms/gemma/permutations.gmi @@ -407,7 +407,18 @@ where K.json has a json["input"] which essentially is above structure. ./bin/gemma-wrapper --keep --force --json --loco --input K.json -- -lmm 9 -g BXD-test.txt -p BXD_pheno_Dave-GEMMA.txt -n 5 -a BXD.8_snps.txt > GWA.json ``` -WIP +Now I have to deal with phenotype files as they are rewritten. We should still cater for `-p` for GEMMA. We already have `--permute-phenotypes filen` for gemma-wrapper. Now we are adding `--phenotypes` to gemma-wrapper which replaces both! +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 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). 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 @@ -420,3 +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) |