Closed bschilder closed 3 years ago
Might be a 'nicer' solution to got with a Bioconductor version of a liftover package: https://www.bioconductor.org/packages/release/workflows/html/liftOver.html it requires GRanges but if we do this as the last step before saving/outputting and not do it by default should be okay
that sounds good too! should be easy enough to convert with MungeSumstats::to_GRanges
Implemented a bioc-based version of this in echoLD with these two functions: https://github.com/RajLabMSSM/echoLD/blob/main/R/liftover.R https://github.com/RajLabMSSM/echoLD/blob/main/R/get_chain_file.R
They seems to be working pretty well. Feel free to copy these over to MungeSumstats
, or I can if you prefer.
Great, be brilliant good to use that here too then!
I don' think I'll have time to get to this in the near future just to let you know in case you need it for some work you're doing.
This has been implemented in 1.1.19
Currently,
MungeSumstats
detects the current genome build but does not do liftover to one genome build or another. Would be awesome to implement this.I extracted the functions needed to do this from XGR, since XGR can be a bit tricky to install and this is the only part I needed for liftover.
https://github.com/RajLabMSSM/echolocatoR/blob/master/R/xLiftOver.R