Chris Wallace
Chris Wallace
Interesting question! sdY is used to scale the prior on the effect size at causal variants. We assume beta comes from a normal distribution with mean 0, and standard deviation...
PP.H4.abf is the primary result. If this is large, then colocalisation is likely. If you believe colocalisation exists, then SNP.PP.H4 tells you which SNP(s) are most likely to be the...
This says there is a 0.026 probability of colocalisation. On the other hand, PP.H3.abf > 0.5, so my interpretation is that there are different causal variants for your two traits...
No, this shouldn't happen because runsusie calls susieR. Could you please share the data for this? -- https://chr1swallace.github.io ________________________________ From: Marcela Johnson ***@***.***> Sent: Tuesday, November 28, 2023 12:55:42 AM...
The z scores in runsusie are beta/sqrt(varbeta) What is the magnitude of your z scores at those snps though? It is very unusual to fine 6 single variant credible sets...
Can you show me str(gwas)? -- https://chr1swallace.github.io ________________________________ From: catheriz ***@***.***> Sent: Thursday, March 7, 2024 8:39:46 PM To: chr1swallace/coloc ***@***.***> Cc: Chris Wallace ***@***.***>; Comment ***@***.***> Subject: Re: [chr1swallace/coloc]...
happy to add to .Rbuildignore, .gitignore, but not sure your Rproj file needs to be in github - won't that affect anyone else downloading the repo to play with who...
Dear Isaac, I can take a look at this, but first, these priors don't make much sense. COuld you try finding a set of priors that meet the requirements here...
The problem is that you are saying the probability exactly 1 SNP is causal for trait 1 is 1. And the probability exactly one SNP is causal for both traits...
I don't know if this is the cause but there is generally an assumption that p12> p1. It's not a hard requirement I don't think, but I might have coded...