Mailman 3 July 2021 - fastlmm-user

New FaST-LMM 0.6.0: Now works with any Python distribution
by Carl K July 21, 2021

July 21, 2021

Greetings, We're happy to announce a new version of FaST-LMM. Version 0.6.0 is easier to install and works with any Python distribution, not just Miniconda. To install: pip uninstall fastlmm (if previously install) pip install fastlmm You can use any Python distribution that supports NumPy. For best performance, be sure your Python distribution includes a fast version of NumPy. We still use Anaconda's Miniconda. As before, FaST-LMM runs under Python 3.7, 3.8, … [View More]

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New version of FaST-LMM
by Carl K July 15, 2021

July 15, 2021

Greetings, I'm happy to announce a new version of FaST-LMM with new features for epistasis. Recall that FaST-LMM allows you to test for epistatic interactions between pairs of SNPs. New: * The output now includes β, the linear coefficient of the epistatic interaction, and its variance. Specifically, the epistatic interaction is the product of standardized and is a fixed effect. Thanks to Ava Khamseh of the University of University of Edinburgh for her derivation of the formula for the … [View More]

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New User-Requested PySnpTools Features
by Carl KADIE July 4, 2021

July 4, 2021

Greetings, I'm happy to announce PySnpTools version 0.5.3. The new features were all at user request. The features are available to any program that uses PySnpTools, including FaST-LMM. The new features are: * The Bed reader can now handle non-numeric chromosome names, for example, "X" and "Y". Likewise, the Bed writer can handle non-numeric chromosomes names. * The Bed reader can now use *.fam and *.bim files with non-standard names. * The SnpMemMap writer can now get data from … [View More]

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I've turned on moderation of the FaST-LMM User mailing list.
by Carl KADIE July 3, 2021

July 3, 2021

Greetings, Sorry for the three recent spam emails to fastlmm-user. I've turned on moderation for this mailing list so there shouldn't be any more. 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…>)

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Release of PySnpTools 0.4.19
by Carl KADIE July 3, 2021

July 3, 2021

Greetings, We're released a new version of PySnpTools (0.4.19). Here are the new features: * Bug fixed in the "Bgen" reader<https://fastlmm.github.io/PySnpTools/#module-pysnptools.distreader>. It has now has been tested on files as large 487,400 individuals x 4,840,000 SNPs (the size of the UK Biobank imputed genotype data). It should work with even larger files. * New option when reading from "Bed"<https://fastlmm.github.io/PySnpTools/#snpreader-bed> files directly into "… [View More]

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New releases of FaST-LMM and PySnpTools
by Carl KADIE July 3, 2021

July 3, 2021

I’m happy to announce a new releases of FaST-LMM<https://pypi.org/project/fastlmm/> and PySnpTools<https://pypi.org/project/pysnptools/>. (This release been my “work” since I retired last summer.) The new releases updates both packages to work with the newest version of Pandas, Numpy, and Scikit-learn. The new FaST-LMM release includes single_snp_scale, which allows FaST-LMM to use a cluster and scale to 1 million individuals. See Kadie and Heckerman, bioRxiv 2018<https://www.… [View More]

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More multiple phenotype support in FaST-LMM
by Carl KADIE July 2, 2021

July 2, 2021

Greetings, I'm happy to announce support for multiple phenotypes by FaST-LMM's single_snp function. Running with more phenotypes can generate more data, so we've also added new features related to caching and filtering out unneeded output lines. A new notebook<https://nbviewer.jupyter.org/github/fastlmm/FaST-LMM/blob/master/doc/ipynb/…> demonstrates all the new features. A university user requested these feature and then used them to do a multi-day run with 16,000 phenotypes. That run … [View More]

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