search

xqwen / dap

software package for integrative genetic association analysis
31 stars 15 forks source link

LD r or r^2 #14

Open matthiasheinig opened 4 years ago

matthiasheinig commented 4 years ago

Hi, from the documentation it does not become entirely clear of LD is to be provided as r (correlation) or r^2. Maybe you could add to your readme how you generate this data for instance with plink (--r or --r2 option)? Thanks a lot for clarifying. Best, Matthias

xqwen commented 4 years ago

Thanks, we will clarify it. It is r, i.e., the off-diagonal elements are signed.

Thanks for the tips on plink! we generate ours using the dap-g built-in -dump_summary option.

William

matthiasheinig commented 4 years ago

Thanks for the prompt reply!