synthetic dataset documentation

fastlmm / FaST-LMM

Python version of Factored Spectrally Transformed Linear Mixed Models

https://fastlmm.github.io/

Apache License 2.0

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synthetic dataset documentation #52

Open snowformatics opened 1 month ago

snowformatics commented 1 month ago

Hi Carl,

can I find somewhere how this synthetic dataset (tests/datasets/synth) was generated (maybe you can share some code) and which of the SNPs should cause an effect? Thanks

CarlKCarlK commented 1 month ago

Greetings, I don't remember how exactly how we created that dataset but here are some tools:

In PySnpTools, the snp_gen utility. https://fastlmm.github.io/PySnpTools/#pysnptools.util.snp_gen
which calls the SnpGen object. https://fastlmm.github.io/PySnpTools/#pysnptools.snpreader.SnpGen
Its use is illustrated in the very beginning of this notebook: https://github.com/fastlmm/FaST-LMM/blob/master/doc/ipynb/heritability_si.ipynb [We then add geo-spatial info.]

-- Carl