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mglev1n / ldscr

LD Score Regression in R
https://mglev1n.github.io/ldscr/
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when trying to use the ldscr analyse, I met the bug. #7

Closed owo12138 closed 1 year ago

owo12138 commented 1 year ago

image

owo12138 commented 1 year ago

If encountering this bug, does it mean there's an issue with my data? How should I self-inspect my data and then improve it?

mglev1n commented 1 year ago

Both the datasets seem to be very old GWAS (more than a decade old), and include relatively small sample sizes. The error indicates that at least one of the traits has negative heritability, and I suspect this lack of heritability is creating a problem when trying to estimate cross-trait heritability. I'd recommend trying to use the original ldsc package (https://github.com/bulik/ldsc), and more broadly using more contemporary/larger GWAS which better capture the heritability of the underlying traits you're interested in.