coloc
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chr1swallace
Repo for the R package coloc
Dear Wallace, A colleague of mine conducted a colocalisation analysis using the coloc.abf() function allowing only 1 causal variant shared between 2 traits. Below is an example script they have...
When I run runsusie() with a "cc" type dataset, the error happened. It works well with a "quant" type dataset.
Hi, First of all, thanks a lot @chr1swallace again for developing coloc - it has been very useful for us to answer many questions we have. A big thanks! I...
Hi I have installed coloc as follows: `install_github("chr1swallace/coloc@main",build_vignettes=F)` If I use "build_vignettes=T" I got the following error: ``` Error: Vignette re-building failed. Execution halted Error: Failed to install 'coloc' from...
Hi, Thank you very much for coloc, it is very helpful! I am wondering, if it is possible to use `runsusie` function for a dataset without varbeta? I am trying...
Hi Chris, You may not think this is helpful, it's just a small change that I thought was helpful when using eQTLgen data, which just has p-values and z-scores (no...
Given users often have issues with out of sample LD matrices causing SuSiE and therefore coloc to give spurious results perhaps we could link to the SuSiE summary statistics paper...
Hi, I would like to ask a question. When I run coloc.abf using coloc version 5.2.3. My input data is as below. type position snp gARE pvalues beta n quant...
Hi all, I am currently conducting post-GWAS analysis and am planning to use Coloc for identifying shared genetic signals for two case/control gwas studies. The gwas were result of GWAS...
Hello, I was wondering why in the runsusie() function convergence must be necessary in order to continue forward with colocalization. I had been running susie with two phenotypes in a...
