How should I use downloaded LD matrix?

YinLiLin / hibayes

:swimmer: Individual-Level, Summary-Level and Single-Step Bayesian Regression Models for Genomic Prediction and Genome-Wide Association Studies

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How should I use downloaded LD matrix? #10

Closed yingji15 closed 3 years ago

yingji15 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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