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fhormoz / caviar

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LD matrix - r or r2? #12

Closed mcgml closed 5 years ago

mcgml commented 5 years ago

Just a quick question - the LD matrix is the pairwise Pearson correlation between two SNPs. Should we provide r or r2?

Thanks Matt

fhormoz commented 5 years ago

The LD matrix should be r.

mcgml commented 5 years ago

thank you

JuRaGa commented 5 years ago

Hi, I am struggling to get the LD matrices. Do you know any quick way of getting these? Thank you, Julia

greengarden0925 commented 5 months ago

Hi, I am struggling to get the LD matrices. Do you know any quick way of getting these? Thank you, Julia

You can do it using local file, refer to :https://cran.r-project.org/web/packages/ieugwasr/vignettes/local_ld.html. Or do it through API https://mrcieu.github.io/ieugwasr/articles/local_ld.html