Hello All,
I was attempting an LDplot using Gpart which has worked for me in the past when using version 4.1. It is not available with the current version of R and I was wondering if anyone has a recommendation for a replacement package or an alternative way of setting up an LDplot.
An obvious alternative is snpStats, if you just want conventional measures of LD. The gpart package implemented Big-LD, which incorporated gene information as well. If you are really interested in that, you could always use the BigLD package, which is the precursor to `gpart', and can be installed directly from GitHub
library(BiocManager)
## may need to install the remotes package as well
##EDIT!
install("sunnyeesl/BigLD")
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version 2.3.6
https://www.bioconductor.org/about/removed-packages/ Gpart was removed in 3.17 because the package maintainers were unresponsive to fixing ERROR in their package. Perhaps someone here can suggest an alternative
Thank you for this!
If anyone knows of an alternative, that would be great.