Greetings,
FaST-LMM 0.6.4 is out. See fastlmm * PyPI<https://pypi.org/project/fastlmm/>
The new version adds show_snp_fract_var_exp as a new option to single_snp.
To install:
pip uninstall fastlmm
pip install fastlmm
Details:
The output will always show 'EffectSize'. If show_snp_fract_var_exp is True, then the output will also show 'SnpFractVarExp'. EffectSize and SnpFractVarExp are different measures of fraction of variance explained. The first uses all variance of the phenotype in the denominator, whereas the second uses variance of the phenotype after removing the effects of population structure and family relatedness. Specifically, EffectSize is SNPWeight^2 * "raw" test SNP variance / phenotype variance, where:
* SNPWeight is the beta for the "standardized test SNP" (where "standardized" means made to have mean 0, stdev 1)
* "raw" means the original test SNP values of "0,1,2" (the count of allele 1 or 2 [it doesn't matter]).
* the phenotype's original values are used (so, they are not, for example, changed by regressing out the covariates).
Yours,
Carl
Carl Kadie, Ph.D.
FaST-LMM & PySnpTools Team<https://fastlmm.github.io/>
(Microsoft Research, retired)
https://www.linkedin.com/in/carlk/
Join the FaST-LMM user discussion and announcement list via email<mailto:fastlmm-user-join@python.org?subject=Subscribe> (or use web sign up<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.pyth…>)
Greetings,
We're happy to announce support for Python 3.10 for the Linux and MacOS versions of FaST-LMM and PySnpTools (but, sadly, not Windows).
The new versions also fixes a problem with reading the BGEN format on newer Python version.
To install:
pip uninstall fastlmm
pip uninstall pysnptools
pip install pysnptools
pip install fastlmm
Yours,
Carl
Carl Kadie, Ph.D.
FaST-LMM & PySnpTools Team<https://fastlmm.github.io/>
(Microsoft Research, retired)
https://www.linkedin.com/in/carlk/
Join the FaST-LMM user discussion and announcement list via email<mailto:fastlmm-user-join@python.org?subject=Subscribe> (or use web sign up<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.pyth…>)
