genoml2

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RafMo20D

During the creation of the virtual environment `# Make virtual env` `conda create -n dev_genoml2 python=3.9` `conda activate dev_genoml2` `# Install GenoML to this` `pip install umap-learn` `pip install .`...

dazweibaum

mkoretsky1

njohnso6

continuous becomes discrete when using umap_reduce

1

https://github.com/GenoML/genoml2/blob/8040f2b1b460cc6085527e5fd65963518459cd11/genoml/__main__.py#L92 When running continuous supervised munge, there is a bug that claims it is discrete, and maybe it is. But clearly, this handler initiates the issue. Also, there is never...

njohnso6

To the casual user, and to me, it isn't immediately clear what to do when not using plink/genotypes/ If I use feature_selection, should I then use the list_features.txt file for...

njohnso6

njohnso6

https://github.com/GenoML/genoml2/blob/8040f2b1b460cc6085527e5fd65963518459cd11/genoml/cli/continuous_supervised_test.py#L45 When run in supervised continuous test I get the error that amounts to cannot find refModel_prefix.joblib I did this rather than a pull request since I know the discrete...

njohnso6

Too many arguments for continuous supervised tune

1

https://github.com/GenoML/genoml2/blob/8040f2b1b460cc6085527e5fd65963518459cd11/genoml/__main__.py#L106 When I run ```genoml continuous supervised tune \ --prefix outputs/``` I get the following error: Traceback (most recent call last): File "/usr/local/lib/python3.7/dist-packages/genoml/__main__.py", line 393, in handle_endpoints endpoint(*args) TypeError: main()...

njohnso6

Need guidance for users on what to do if fewer than 100 samples?

1

https://github.com/GenoML/genoml2/blob/8040f2b1b460cc6085527e5fd65963518459cd11/genoml/__main__.py#L92 Perhaps don't make 100 samples hardwired? Or at least more guidance in the documentation.

njohnso6