question about PP.H3

[EchoLee0925]

I have used the function coloc.sbf(), but can't get the the posterior probability SNP.PP.H3 of the single SNP . So how to get the SNP.PP.H0, SNP.PP.H1,SNP.PP.H2 and SNP.PP.H3， not only the summary information.

[chr1swallace]

There is no single SNP posterior, just a set of snp pairs. What do you want this for?

https://chr1swallace.github.io

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From: EchoLee0925 @.> Sent: Thursday, December 23, 2021 7:24:07 AM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] question about PP.H3 (Issue #68)

I have used the function coloc.sbf(), but can't get the the posterior probability SNP.PP.H3 of the single SNP . So how to get the SNP.PP.H0, SNP.PP.H1,SNP.PP.H2 and SNP.PP.H3， not only the summary information.

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/68, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2BHN3DGUXFWW4IXC5TUSLFBPANCNFSM5KUFA2QQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://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 are subscribed to this thread.Message ID: @.***>

[EchoLee0925]

sorry, I want a set of snp-gene pairs. My trait1 is GWAS, trait 2 is eQTL.

[EchoLee0925]

I used the function coloc.abf()

[chr1swallace]

What would you use the SNP pair posterior for though?

https://chr1swallace.github.io

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From: EchoLee0925 @.> Sent: Thursday, December 23, 2021 9:31:52 AM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] question about PP.H3 (Issue #68)

I used the function coloc.abf()

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/68#issuecomment-1000166292, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2HO2UXGBHYLJGGREKLUSLUARANCNFSM5KUFA2QQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://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 commented.Message ID: @.***>

[EchoLee0925]

I want to konw the H0-H4, especially the H3 and H4. So can you tell me the method to get them? Besides, I read some articals, they also give these values.

[chr1swallace]

can you explain why though? or quote the articles?

you get posteriors for H0-H4. You are asking for snp pair posteriors conditional on H3 being true (I think). If I understand what you want to use them for I might be able to suggest something more appropriate to use.

On Thu, 2021-12-23 at 15:59 -0800, EchoLee0925 wrote:

I want to konw the H0-H4, especially the H3 and H4. So can you tell me the method to get them? Besides, I read some articals, they also give these values. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: @.***>

[EchoLee0925]

Yes, I want to know the relationship between the snp pair, whether coloc or individual, but now I can't get the H3. Besides, I have another problem. I have one same snp pair in two datasets, which means rs1--gene1 in data1, rs1--gene1 in data2. When I input data1 and data2 in the coloc.abf function individual, it got total different results. I don't understand, because rs1--gene1 parameter is same in the data1 and data2, why the results is various? And when I only put the rs1-gene1,not include other snp-pair, the result is also different. I feel confuesd.

[chr1swallace]

I'm afraid I still can't understand your question. Did you look at the documentation, eg http://chr1swallace.github.io/coloc/articles/a03_enumeration.html ?

https://chr1swallace.github.io

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From: EchoLee0925 @.> Sent: Wednesday, December 29, 2021 2:55:54 AM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] question about PP.H3 (Issue #68)

Yes, I want to know the relationship between the snp pair, whether coloc or individual, but now I can't get the H3. Besides, I have another problem. I have one same snp pair in two datasets, which means rs1--gene1 in data1, rs1--gene1 in data2. When I input data1 and data2 in the coloc.abf function individual, it got total different results. I don't understand, because rs1--gene1 parameter is same in the data1 and data2, why the results is various? And when I only put the rs1-gene1,not include other snp-pair, the result is also different. I feel confuesd.

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/68#issuecomment-1002371407, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2EVAINA57DWYLQ633LUTJ2DVANCNFSM5KUFA2QQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://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 commented.Message ID: @.***>

[EchoLee0925]

I see it carefully. But your documentation also just show the SNP.PP.H4, which can't see the PP.H3. But in your artical , how did you get the PP.H3? I just want to know the PP.H3. Besides, the another question is the same snp pair in two gene locus, why it had same beta,se,p and maf for GWAS and eQTL, it actually get different PP.H4?

[chr1swallace]

If you print the return value, the PP3 is part of it.

I can't answer questions about your data without seeing your data and the cinema you run

https://chr1swallace.github.io

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From: EchoLee0925 @.> Sent: Wednesday, December 29, 2021 9:49:56 AM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] question about PP.H3 (Issue #68)

I see it carefully. But your documentation also just show the SNP.PP.H4, which can't see the PP.H3. But in your artical , how did you get the PP.H3? I just want to know the PP.H3. Besides, the another question is the same snp pair in two gene locus, why it had same beta,se,p and maf for GWAS and eQTL, it actually get different PP.H4?

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/68#issuecomment-1002509182, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2DNW4C2PYW365CSC6DUTLKUJANCNFSM5KUFA2QQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://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 commented.Message ID: @.***>

[chr1swallace]

Sorry, data not cinema

https://chr1swallace.github.io

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From: Chris Wallace @.> Sent: Wednesday, December 29, 2021 5:01:56 PM To: chr1swallace/coloc @.>; chr1swallace/coloc @.> Cc: Comment @.> Subject: Re: [chr1swallace/coloc] question about PP.H3 (Issue #68)

If you print the return value, the PP3 is part of it.

I can't answer questions about your data without seeing your data and the cinema you run

https://chr1swallace.github.io

---

From: EchoLee0925 @.> Sent: Wednesday, December 29, 2021 9:49:56 AM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] question about PP.H3 (Issue #68)

I see it carefully. But your documentation also just show the SNP.PP.H4, which can't see the PP.H3. But in your artical , how did you get the PP.H3? I just want to know the PP.H3. Besides, the another question is the same snp pair in two gene locus, why it had same beta,se,p and maf for GWAS and eQTL, it actually get different PP.H4?

— Reply to this email directly, view it on GitHubhttps://github.com/chr1swallace/coloc/issues/68#issuecomment-1002509182, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AAQWR2DNW4C2PYW365CSC6DUTLKUJANCNFSM5KUFA2QQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://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 commented.Message ID: @.***>

[EchoLee0925]

I had print, but it only include the summary for PP3. But as you said ,I want to get the PP3 for snp-pair. Can you give me a e-mail address, I can show the picture of my data and result. The address you leave in the coloc paper, I send a mail, but still not get response.

[EchoLee0925]

I have another question. How to know the H3 or H4 being true, which value to judge?

[chr1swallace]

the PP3 for snp pair is never calculated. I don't understand what you want it for. If you believe H3 is true, then just take the fine mapping results for each trait independently

On Wed, 2021-12-29 at 17:37 -0800, EchoLee0925 wrote:

I had print, but it only include the summary for PP3. But as you said ,I want to get the PP3 for snp-pair. Can you give me a e-mail address, I can show the picture of my data and result. The address you leave in the coloc paper, I send a mail, but still not get response. — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: @.***>

[chr1swallace]

They are posterior probabilities. There is no cut off where we would say one is definitely true.

On Wed, 2021-12-29 at 19:37 -0800, EchoLee0925 wrote:

I have another question. How to know the H3 or H4 being true, which value to judge? — Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you commented.Message ID: @.***>