search

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
187 stars 90 forks source link

Extract the exact snps included in the best model #285

Closed Fnyasimi closed 2 years ago

Fnyasimi commented 2 years ago

@choishingwan Thanks for the nice software.

I am wondering is there a way to extract the SNPs used in the best model instead of just the number of SNPs? I would like to find the specific SNPs for further analysis and mapping for downstream process. What would be the best way to extract these individual SNPs from the best fit model?

choishingwan commented 2 years ago

--print-snp

You will need to filter by p-value though.

On Fri, Dec 17, 2021 at 1:23 PM Fnyasimi @.***> wrote:

@choishingwan https://github.com/choishingwan Thanks for the nice software.

I am wondering is there a way to extract the SNPs used in the best model instead of just the number of SNPs? I would like to find the specific SNPs for further analysis and mapping for downstream process. What would be the best way to extract these individual SNPs from the best fit model?

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/285, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYTP5PO46ZB2OIMDNI3URN5ZBANCNFSM5KJOC2TQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

Fnyasimi commented 2 years ago

The threshold p-value right. Thanks

choishingwan commented 2 years ago

correct

On Fri, Dec 17, 2021 at 1:29 PM Fnyasimi @.***> wrote:

The threshold p-value right. Thanks

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/285#issuecomment-996931694, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYXKSUM3NKIMTQJPQKTURN6QVANCNFSM5KJOC2TQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>

Fnyasimi commented 2 years ago

Thank you

michellekee commented 2 years ago

Hi, when filtering for the best p-value threshold ( aka pT) to obtain the SNP list , do we filter as p < pT or p <= pT?

choishingwan commented 2 years ago

<=

On Sun, Mar 13, 2022 at 10:24 PM Michelle @.***> wrote:

Hi, when filtering for the best p-value threshold ( aka pT) to obtain the SNP list , do we filter as p < pT or p <= pT?

— Reply to this email directly, view it on GitHub https://github.com/choishingwan/PRSice/issues/285#issuecomment-1066272836, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJTRYUCVSAZ6NZXLLUO3ELU72PMVANCNFSM5KJOC2TQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

You are receiving this because you were mentioned.Message ID: @.***>