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choishingwan / PRSice

A software package for calculating, applying, evaluating and plotting the results of polygenic risk scores
http://prsice.info
GNU General Public License v3.0
182 stars 86 forks source link

.psam files #156

Closed sarasaezALS closed 5 years ago

sarasaezALS commented 5 years ago

Hi Sam, I am trying to rung PRSice2 using WGS data and our binary files are in .psam format (from PLINK2). could they be used as a imput?

choishingwan commented 5 years ago

Unfortunately no, I simply don't have time to implement supports for more than two format... You will either need to change it into bgen or bed format instead.

Dr Shing Wan Choi Postdoctoral Fellow Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

On Tue, Oct 1, 2019 at 10:58 AM sarasaezALS notifications@github.com wrote:

Hi Sam, I am trying to rung PRSice2 using WGS data and our binary files are in .psam format (from PLINK2). could they be used as a imput?

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sarasaezALS commented 5 years ago

OK, WILL DO! THANKS

choishingwan commented 5 years ago

I have recently (yesterday) received a bug report suggesting that the logistic regression used by PRSice is somewhat problematic (since v 2.2.5). Upon further investigation, that is indeed the case and the problem is currently fixed (by using another less efficient algorithm). This might solve your problem. Am now running tests on the latest code (which constitute huge changes in the underlying structure of PRSice), and the update should be release once I am confident that most of the functionality of the new code base are working properly.

Thank you

Sam

On Tue, Oct 1, 2019 at 12:16 PM sarasaezALS notifications@github.com wrote:

OK, WILL DO! THANKS

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/156?email_source=notifications&email_token=AAJTRYQQHXQDVNZPTKRZRETQMNZW3A5CNFSM4I4KXVSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAB265A#issuecomment-537112436, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJTRYTBI5IZNPB36DOH4U3QMNZW3ANCNFSM4I4KXVSA .

sarasaezALS commented 5 years ago

Hi Sam, Will the new version incorporate the p-competitive? …………………………………… Sara Saez-Atienzar PhD Postdoctoral Research Fellow Neuromuscular Diseases Research Section Laboratory of Neurogenetics, NIA, NIH 35 Convent Drive, Room 1A-108, Bethesda, MD 20892-3707

From: Shing Wan Choi notifications@github.com Reply-To: choishingwan/PRSice reply@reply.github.com Date: Thursday, October 3, 2019 at 4:39 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: "Saez, Sara (NIH/NIA/IRP) [F]" sara.saez@nih.gov, Author author@noreply.github.com Subject: Re: [choishingwan/PRSice] .psam files (#156)

I have recently (yesterday) received a bug report suggesting that the logistic regression used by PRSice is somewhat problematic (since v 2.2.5). Upon further investigation, that is indeed the case and the problem is currently fixed (by using another less efficient algorithm). This might solve your problem. Am now running tests on the latest code (which constitute huge changes in the underlying structure of PRSice), and the update should be release once I am confident that most of the functionality of the new code base are working properly.

Thank you

Sam

On Tue, Oct 1, 2019 at 12:16 PM sarasaezALS notifications@github.com wrote:

OK, WILL DO! THANKS

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/156?email_source=notifications&email_token=AAJTRYQQHXQDVNZPTKRZRETQMNZW3A5CNFSM4I4KXVSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAB265A#issuecomment-537112436, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJTRYTBI5IZNPB36DOH4U3QMNZW3ANCNFSM4I4KXVSA .

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choishingwan commented 5 years ago

I won't delete that function. So that should be there.

sarasaezALS commented 5 years ago

Perfect!!!!

…………………………………… Sara Saez-Atienzar PhD Postdoctoral Research Fellow Neuromuscular Diseases Research Section Laboratory of Neurogenetics, NIA, NIH 35 Convent Drive, Room 1A-108, Bethesda, MD 20892-3707

From: Shing Wan Choi notifications@github.com Reply-To: choishingwan/PRSice reply@reply.github.com Date: Monday, October 7, 2019 at 4:26 PM To: choishingwan/PRSice PRSice@noreply.github.com Cc: "Saez, Sara (NIH/NIA/IRP) [F]" sara.saez@nih.gov, Author author@noreply.github.com Subject: Re: [choishingwan/PRSice] .psam files (#156)

I won't delete that function. So that should be there.

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