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chr1swallace / coloc

Repo for the R package coloc
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Varbeta for eQTL and GWAS dataset #108

Closed HKJ396 closed 1 year ago

HKJ396 commented 1 year ago

Hi, I have a question about varbeta which I take it to be the variance. I have found the variance for my GWAS results calculated from standard error. For example,I worked out the Standard deviation (SD) from standard error of the coefficient reported for each SNP result and then worked out variance from SD. Do I need to find the varbeta for the GTEX data in the same way? It only gives me standard error of the slope? So I am assuming I will need to find the variance/varbeta as well?

chr1swallace commented 1 year ago

varbeta is simply the square of the standard error of beta. you don't need the SD.

https://chr1swallace.github.io

From: HKJ396 @.> Sent: 28 November 2022 11:39 To: chr1swallace/coloc @.> Cc: Subscribed @.***> Subject: [chr1swallace/coloc] Varbeta for eQTL and GWAS dataset (Issue #108)

Hi, I have a question about varbeta which I take it to be the variance. I have found the variance for my GWAS results calculated from standard error. For example,I worked out the Standard deviation (SD) from standard error of the coefficient reported for each SNP result and then worked out variance from SD. Do I need to find the varbeta for the GTEX data in the same way? It only gives me standard error of the slope? So I am assuming I will need to find the variance/varbeta as well?

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchr1swallace%2Fcoloc%2Fissues%2F108&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7Ce486f1848eed40f3746108dad13537d5%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638052323739388891%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wYIX9oeyLkLojmFLIdqS8Jh%2BEn%2B6DdACALFgnv9qGeI%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAQWR2BLUNUQAETBBAOQ7JLWKSKXFANCNFSM6AAAAAASNHM5KQ&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7Ce486f1848eed40f3746108dad13537d5%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638052323739388891%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=wnc4t38jX03u3iOg5jV%2F5vPUhz%2BgRfGnLqaeOX0Jipg%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

HKJ396 commented 1 year ago

Thank you! I'm assuming I do SE^2 to find varbeta for the eqtl dataset too, since it gives me slope_se?

chr1swallace commented 1 year ago

Yes

https://chr1swallace.github.io

From: HKJ396 @.> Sent: Monday, November 28, 2022 12:54:32 PM To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] Varbeta for eQTL and GWAS dataset (Issue #108)

Thank you! I'm assuming I do SE^2 to find varbeta for the eqtl dataset too, since it gives me slope_se?

— Reply to this email directly, view it on GitHubhttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fchr1swallace%2Fcoloc%2Fissues%2F108%23issuecomment-1329043740&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C9b47a9b17e8a4fab20fb08dad13fc4a8%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638052369052880210%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=kHtmAjRYqFjOEfITtbi1WRVi30I8DQNcrBFRil5Y8js%3D&reserved=0, or unsubscribehttps://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAAQWR2DG4B2FLD65TF3VYVTWKSTQRANCNFSM6AAAAAASNHM5KQ&data=05%7C01%7Ccew54%40universityofcambridgecloud.onmicrosoft.com%7C9b47a9b17e8a4fab20fb08dad13fc4a8%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638052369052880210%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=WHxh7Nvm0gepQLW6WzposuwJRZwNA3N6ZBwhO00ZEyE%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>

HKJ396 commented 1 year ago

I have my combined GWAS SNPs of interest and eQTL data with beta, varbeta, MAF, n. of people in study, SE, P value for my both the GWAS and the eQTL. I have also got a seperate LD matrix generated from my GWAS SNPs of interest. E.g. 

CHR_A   BP_A   SNP_B           R2       SNP_A  CHR_B         BP_B                                                                             
1     18054638 rs1572792:18054785:G:A     0.407277   rs35592535:18054638:GC:G      1     18054785

Do I need to reference my LD matrix separately in the coloc.susie function or incorporate the LD values in my GWAS-eQTL dataset? Does the SNPs in the LD matrix, need to be in the same order in the GWAS-eQTL dataset?

Thanks in advance

chr1swallace commented 1 year ago

please check this http://chr1swallace.github.io/coloc/articles/a02_data.html and let me know if you have questions it doesn't anwer [https://chr1swallace.github.io/coloc/logo.png]http://chr1swallace.github.io/coloc/articles/a02_data.html Coloc: data structures • coloc - GitHub Pageshttp://chr1swallace.github.io/coloc/articles/a02_data.html Data structures. The enumeration approaches to coloc coloc.abf and coloc.susie require the same data format. To be flexible, coloc.abf allows a wider variety of inputs, which can sometimes be confusing. This document aims to set out what ideal and acceptable data structures are, as well as covering some points on how you should select the SNPs for study. chr1swallace.github.io

https://chr1swallace.github.io

From: HKJ396 @.> Sent: 29 November 2022 11:31 To: chr1swallace/coloc @.> Cc: Chris Wallace @.>; Comment @.> Subject: Re: [chr1swallace/coloc] Varbeta for eQTL and GWAS dataset (Issue #108)

I have my combined GWAS SNPs of interest and eQTL data with beta, varbeta, MAF, n. of people in study, SE, P value for my both the GWAS and the eQTL. I have also got a seperate LD matrix generated from my GWAS SNPs of interest. E.g.

CHR_A BP_A SNP_B R2 SNP_A CHR_B BP_B 1 18054638 rs1572792:18054785:G:A 0.407277 rs35592535:18054638:GC:G 1 18054785

Do I need to reference my LD matrix separately in the coloc.susie function or incorporate the LD values in my GWAS-eQTL dataset? Does the SNPs in the LD matrix, need to be in the same order in the GWAS-eQTL dataset?

Thanks in advance

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