how to handle ldsc with negative h2 value?

privefl / bigsnpr

R package for the analysis of massive SNP arrays.

https://privefl.github.io/bigsnpr/

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how to handle ldsc with negative h2 value? #506

Open SangGold opened 4 days ago

SangGold commented 4 days ago

when i run LDpred2 with gwas of biobank Japan for parkinson disease and target genotypes data is 504 samples of EAS in 1KGP, it raise an error: ldsc h2 estimate value is negative (h2 = -0.000936). I don't know why and how to fix it, could you help me resolve this problem?! Thank you so much!

privefl commented 4 days ago

h2 estimates from ldsc can be negative, there is no error there; if you actually got an error, please report the precise error message Then, either the trait you're looking at has a very very small heritability, or the matching between LD scores and chi square stats is incorrect.