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TalShor / SciLMM

Sparse Cholesky factorIzation Linear Mixed model
GNU General Public License v3.0
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Questions about usage #11

Open ryansmith23 opened 4 years ago

ryansmith23 commented 4 years ago

Hi all,

First I want to thank you for your hardwork on this python package. You guys have put together a solution that will be a big help for the issues me and my team have been facing.

We have recently been testing out this package for use with our population and have had success calculating the IBD so far. We're now working to fit the LMM but are somewhat confused with how to use the package. Is the script SciLMM.py now deprecated? I see that the SparseCholesky.py file has an implementation for HE and LMM that is somewhat similar to the files in the Estimation directory. Is this the recommended script to use? What is the difference between this and the existing code in the Estimation directory.

Thank you

omerwe commented 4 years ago

Hi Ryan,

We're glad you found our work useful! Thanks for your commit --- they look great, we'll probably merge them soon.

Indeed, I believe that SciLMM.py is deprecated. Unfortunately the author of the code is busy in industry and has little time to maintain the package nowadays... We may get around to cleaning it at some point, but for now I recommend that you follow the examples in the script test_ibdCompute.py https://github.com/TalShor/SciLMM/blob/master/scilmm/Tests/test_IBDCompute.py, which is the recommended way to run Sci-LMM.

On Tue, Dec 3, 2019 at 1:32 PM Ryan Smith notifications@github.com wrote:

Hi all,

First I want to thank you for your hardwork on this python package. You guys have put together a solution that will be a big help for the issues me and my team have been facing.

We have recently been testing out this package for use with our population and have had success calculating the IBD so far. We're now working to fit the LMM but are somewhat confused with how to use the package. Is the script SciLMM.py now deprecated? I see that the SparseCholesky.py file has an implementation for HE and LMM that is somewhat similar to the files in the Estimation directory. Is this the recommended script to use? What is the difference between this and the existing code in the Estimation directory.

Thank you

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ryansmith23 commented 4 years ago

Hey Omer,

Thanks for the update! I figured that was the case with SciLMM.py and will follow the examples from the tests.

Once we finish our testing I'll spend some more time cleaning up the codebase. I'll create a proper pull request then that you guys can consider. I'll be in touch in the next few days.