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genetics-statistics / faster_lmm_d

A faster lmm for GWAS. Supports GPU backend.
GNU General Public License v3.0
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Linear Regression and Logistic Regression #36

Open prasunanand opened 6 years ago

prasunanand commented 6 years ago

Linear Regression has been implemented on single core.

Exact same output upto 6 decimal places :D . To test

./build/faster_lmm_d --geno=data/gemma/BXD_geno.txt.gz --pheno=data/gemma/BXD.pheno --covar=data/gemma/BXD_covariates2.txt --anno=data/gemma/BXD_snps.txt --kinship=data/gemma/BXD.cXX.txt --lm=4 --maf=0.1 --cmd=lm

Logistic Regression needs to be implemented. I have ported the code. @pjotrp : Currently, GEMMA uses code in logistic.cpp for BSLMM-DAP.

I think logistic regression as a GWAS test has not been implemented into GEMMA. What should I do?

prasunanand commented 6 years ago

Linear Models implemented on multi-core as well as GPUs . https://github.com/prasunanand/faster_lmm_d/commit/6f92135835fdaab5d98bc6a052f0018261a981f2

GPUs and Multicore are faster. Will report timings soon.

prasunanand commented 6 years ago

Logistic Regression has been implemented :smile:

https://github.com/prasunanand/faster_lmm_d/commit/379db6720c8682ec4fe481fa93ddf2447c07fd10

Plugging in GEMMA IO is in progress.

robwwilliams commented 6 years ago

Great work Prasun. Enjoyed talking yesterday.

On Tue, Jul 17, 2018 at 3:13 PM Prasun Anand notifications@github.com wrote:

Logistic Regression has been implemented 😄

prasunanand@379db67 https://github.com/prasunanand/faster_lmm_d/commit/379db6720c8682ec4fe481fa93ddf2447c07fd10

Plugging in GEMMA IO is in progress.

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prasunanand commented 6 years ago

Thanks @robwwilliams :) . I too enjoyed the meeting.