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omerwe / polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)
MIT License
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max_num_causal=1 #92

Closed gbloeb closed 2 years ago

gbloeb commented 2 years ago

I'm confused by this warning: When max_num_causal=1 fine-mapping please omit the flags --geno and --ld (we cannot use LD information in that setting)

Why wouldn't you be able to use LD information when max_num_causal=1? Thanks!

omerwe commented 2 years ago

Hi @gbloeb,

This is counter-intuituve, but most fine-mapping models do not require summary LD information when assuming only a single causal SNP per locus. You can read more about it in the PolyFun paper, and there's a mathematical proof in the Supplementary note (in the section called PolyFun + SuSiE does not make use of summary LD information when restricting to a single causal SNP per locus).