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GenoML / genoml2

GenoML (genoml2) is an open source Python package. It is an automated machine learning (autoML) platform for genomics data
Apache License 2.0
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Controlling stringency of r^2 in PLINK's pruning step during munging #17

Closed m-makarious closed 3 years ago

m-makarious commented 3 years ago

Please make sure that this is a feature request.

System information:

Describe Current Behavior/State and Recommended Feature Request: Right now, there's just a default, stringent cut-off for PLINK. Should change this so the default is not stringent, but that the user can tweak it.

Will this change the current API? How? Yup, will include another flag under munging

Who Will Benefit from this Feature? Geneticists who get picky about pruning :)

Any Additional Information?

m-makarious commented 3 years ago

The user now during the munging step use the --r2_cutoff flag to change the PLINK stringency. Available options are 0.1, 0.2, 0.3, 0.4, and 0.5... with 0.5 being the current default.

Thank you for suggesting this, @mikeDTI !

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