coloc
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chr1swallace
Repo for the R package coloc
https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html In the article, the example provided by the author, there are two rows in the result of susie.res$summary. nsnps hit1 hit2 PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf 1: 500 s105 s105...
This is the corrected version for single-SNP credible sets. I also changed authorship to give Chris Wallace due credit.
Hi Chris, I have learned to use the coloc you developed recently. It is a very useful tool. And I got some questions when I use this package. When we...
combine.abf() function has a useful "quiet=FALSE" parameter. Unfortunately, It is not possible to pass this parameter when calling coloc.abf() (which internally calls combine.abf). Suggestion: https://github.com/chr1swallace/coloc/blob/0afe6070a02d571f038c4f6269e1f36842aaa34f/R/claudia.R#L324-L325 ``` coloc.abf
Hello, I am constantly receiving this error once I want to check my data structure: Error in if (min(p) > warn.minp) warning("minimum p value is: ", format.pval(min(p)), : missing value...
Could you please help with the following error message. I am attempting to execute COLOC on two GWAS summary statistics. However, when I try to run COLOC using the code...
Hi Chris, I have SuSiE results for a large number of GWAS traits and a larger number of e/sQTL signals from a range of tissues, and am using these for...
I conducted co-localization analysis of eQTL and GWAS using the coloc package with the following code: result = 1, setting p1=1/(nsnps + 1) 2: In adjust_prior(p2, nrow(df2), "2") : p2...
On the page https://chr1swallace.github.io/coloc/articles/a06_SuSiE.html, there is a paragraph like this: > With these susie output objects stored, we can colocalise every pair of signals. This analysis says the first pair,...
This commit add the necessary files/new lines in existing files to enable me to edit coloc using RStudio.
