synthetic dataset documentation

[snowformatics]

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]

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