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.
This update (version 5) supercedes previously published version 4 by introducing use of the SuSiE approach to deal with multiple causal variants rather than conditioning or masking. See
Wang, G., Sarkar, A., Carbonetto, P., & Stephens, M. (2020). A simple new approach to variable selection in regression, with application to genetic fine mapping. Journal of the Royal Statistical Society: Series B (Statistical Methodology). https://doi.org/10.1111/rssb.12388
for the full SuSiE paper and
Wallace (2021). A more accurate method for colocalisation analysis allowing for multiple causal variants. bioRxiv https://www.biorxiv.org/content/10.1101/2021.02.23.432421v1
for a description of its use in coloc.
To install from R, do
if(!require("remotes"))
install.packages("remotes") # if necessary
library(remotes)
install_github("chr1swallace/coloc",build_vignettes=TRUE)Note that in all simulations, susie outperforms the earlier
conditioning approach, so is recommended. However, it is also new code,
so please consider the code “beta” and let me know of any issues that
arise - they may be a bug on my part. If you want to use it, the
function you want to look at is coloc.susie. It can take
raw datasets, but the time consuming part is running SuSiE. coloc runs
SuSiE and saves a little extra information using the
runsusie function before running an adapted colocalisation
on the results. So please look at the docs for runsusie
too. I found a helpful recipe is 1. Run runsusie on dataset
1, storing the results 2. Run runsusie on dataset 2,
storing the results 3. Run coloc.susie on the two outputs
from above
More detail is available in the vignette a06_SuSiE.html accessible by
vignette("a06_SuSiE",package="coloc")For usage, please see the vignette at https://chr1swallace.github.io/coloc
Key previous 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) - Thoughts about priors in coloc are described in Wallace C (2020) Eliciting priors and relaxing the single causal variant assumption in colocalisation analyses. PLOS Genetics 16(4): e1008720
see FAQ
to generate website: https://chr1swallace.github.io/coloc/
Rscript -e "pkgdown::build_site()"