Adjuster and UMAP separately?

[m-makarious]

Please make sure that this is a feature request.

System information:

• GenoML Version: v1.0.0.beta-5
• GenoML Installed from (source or binary): Source
• Are you willing to contribute to this request? (Yes/No): ...yes

Describe Current Behavior/State and Recommended Feature Request: Right now, the way adjusting your data works is unclear and does not allow for people to

• reduce using UMAP only, or
• option to not use UMAP reduction, but to still adjust and normalize, or
• option to adjust without normalizing

Will this change the current API? How? Will change and add flags to make these options possible

Who Will Benefit from this Feature? ...everyone, I hope

Any Additional Information?

[m-makarious]

Didn't really like the name --target_columns, so changing that flag to be --target_features instead :) Other arguments pertaining to this will be:

• --umap_reduce: a yes/no option
• --adjust_data: a yes/no option
• --adjust_normalize: a yes/no option contingent on the previous flag
• --target_features: a string (file) input for a .txt file with a list of features found in the munged set, contingent on the previous flag
• --confounders: a string (file) input for a .csv file with confounders to adjust the data for, contingent on previous flags

The returned product is an updated .dataForML file that replaces what was at your --prefix input.

The README has been updated to reflect this change and will be reflected in the next release.