Adjust genotypes for tSNE/UMAP/PC loadings

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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Adjust genotypes for tSNE/UMAP/PC loadings #11

Closed mikeDTI closed 4 years ago

mikeDTI commented 4 years ago

Please make sure that this is a feature request.

System information:

GenoML Version: 1.5
GenoML Installed from (source or binary): source
Are you willing to contribute to this request? (Yes/No): yep, I guess

Describe Current Behavior/State and Recommended Feature Request: Adjust genotypes to be scores at munge. This is already common in preprocessing of RNAseq data. A way to account for population substructure in genotypes for repeated use in ML.

Will this change the current API? How? Extra munge option.

Who Will Benefit from this Feature? Anyone getting beat up by population stratification.

Any Additional Information? Dogs do not like thunderstorms.

mikeDTI commented 4 years ago

I'm also going to add a quick PCs versus outcome module to check for population stratification and if it needs to be adjusted for.

mikeDTI commented 4 years ago

😬😵

On Thu, Aug 6, 2020 at 5:41 PM Mary B. Makarious notifications@github.com wrote:

Assigned #11 https://github.com/GenoML/genoml_v2/issues/11 to @mikeDTI https://github.com/mikeDTI.

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m-makarious commented 4 years ago

New version of package now has this - look at README for additional help and update pip package using pip install genoml2 --upgrade