Runsusie returns null credible set

[jeji0209]

Hello. When I try runsusie() with a set of SNPs before running coloc.susie(), it ways that my variants have converged at max iterations 100. However, when I check my result for runsusi() by using summary(susie_result), it returns that I have 0 credible sets, and 0 variables for credible sets. How can interpret this?

Thank you.

[chr1swallace]

Do you have any strong associations? Perhaps there is no causal variant in the region?

https://chr1swallace.github.io

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From: jeji0209 @.> Sent: Thursday, June 23, 2022 10:05:15 AM To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] Runsusie returns null credible set (Issue #94)

Hello. When I try runsusie() with a set of SNPs before running coloc.susie(), it ways that my variants have converged at max iterations 100. However, when I check my result for runsusi() by using summary(susie_result), it returns that I have 0 credible sets, and 0 variables for credible sets. How can interpret this?

Thank you.

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchr1swallace%2Fcoloc%2Fissues%2F94&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C6b24daa5c1a54ba4a16408da54f77e76%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637915719190288082%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sFCRMKzrJTOSDk%2F%2BoIUbheIN%2BNK2DQXEnhOtnYuCPhg%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAQWR2GTD4Z3NYUR35KTBKTVQQSEXANCNFSM5ZTSPRRQ&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C6b24daa5c1a54ba4a16408da54f77e76%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637915719190288082%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fnfPU1IIDf9nBdUOtrqwZHcRHb%2FmWbyXu70uLrNrym0%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[jeji0209]

Ah yes now I see. The variants are in strong association overall (when I checked the R2 value, its mean is above 0.8), but when I cut them by significant p-value (0.05), those variants aren't in high correlation. If I am understanding correctly, these variants won't merge into a credible set?

[chr1swallace]

0.05 is not considered significant in genetic association. what is your minimum p value?

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From: jeji0209 @.> Sent: 23 June 2022 12:01 To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] Runsusie returns null credible set (Issue #94)

Ah yes now I see. The variants are in strong association overall (when I checked the R2 value, its mean is above 0.8), but when I cut them by significant p-value (0.05), those variants aren't in high correlation. If I am understanding correctly, these variants won't merge into a credible set?

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[jeji0209]

It varies depending on the variant set I am using (none of them are returning a credible set so far), but the lowest one had 0.001.

[chr1swallace]

Well you have nothing that would be considered genome wide significant

https://chr1swallace.github.io

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From: jeji0209 @.> Sent: Thursday, June 23, 2022 12:32:12 PM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] Runsusie returns null credible set (Issue #94)

It varies depending on the variant set I am using (none of them are returning a credible set so far), but the lowest one had 0.001.

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[jeji0209]

Ah okay I understand!