LD D-prime (D') calculation

Question

[Javier]

Hi all,

I am trying to compute LD statistics with gaston package in R and plotting them, but I do not know how to obtain D' values. I do obtain r2 and D values but I would very interested in D' statistic. Is it possible to calculate it? Do you know another resource in order to do it?

I tried Haploview but it seems that there is an error exporting the images and Snpstats/Snpmatrix packages are not working because they are not available to install.

Many thanks

Answer 1

[bk11]

You can try LDlinkR

https://cran.r-project.org/web/packages/LDlinkR/vignettes/LDlinkR.html