The coloc package can be used to perform genetic colocalisation analysis of two potentially related phenotypes, to ask whether they share common genetic causal variant(s) in a given region.
For usage and background, see the vignette at https://chr1swallace.github.io/coloc
Key references are:
- original propostion of proportional colocalisation Plagnol et al (2009)
- proportional colocalisation with type 1 error rate control Wallace et al (2013)
- colocalisation by enumerating all the possible causal SNP configurations between two traits, assuming at most one causal variant per trait Giambartolomei et al (2013)
cp vignettes/colocqq-tests.R.tospin vignettes/colocqq-tests.R && Rscript -e 'knitr::spin("vignettes/colocqq-tests.R",knit=FALSE); devtools::build_vignettes()'
https://chr1swallace.github.io/coloc/
Rscript -e "pkgdown::build_site()"