How should I use downloaded LD matrix?

[yingji15]

Hi there,

Thanks for making this available!
I am wondering if I can use LD matrix downloaded from (https://zenodo.org/record/3350914#.X94SHOn0lBx ) instead of computing by myself. For example, can I specify the path to this LD matrices and run SBayesR using hibayes package?

ldm1 = read("xx") # path to downloaded LD matrix
fit = sbayes(sumstat=sumstat, ldm=ldm1, model="SBayesR", niter=20000, nburn=10000, outfreq=10, verbose=TRUE)

Thanks!

Ying

[YinLiLin]

Hi Ying,

Thank you for trying hibayes.
Sorry that hibayes could not use the LD matrix computed by GCTB, as hibayes uses different types of LD matrix. I just wondering why not use GCTB directly?

Best,
Lilin

[yingji15]

Hi Lilin,
Thank you so much for your reply! Yes I initially I tried the latest version of GCTB (2.02) but it didn't work in my current environment. So I was looking for other implementations online. I found GCTB (2.0) works in my environment. Thank you so much!

Best,
Ying