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gkichaev / PAINTOR_V3.0

Fast, integrative fine mapping with functional data
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Matching alleles with reference panel #8

Closed Kyoko-wtnb closed 7 years ago

Kyoko-wtnb commented 7 years ago

Hi,

Firstly, I really appreciate the very clear documentations and the software works perfectly.

However, I have got a question about allele matching with reference panel. If I understand correctly, the model does not take into account that which allele is the effect allele, since the minimum inputs are Z score and r2 matrix. And direction of Z score represents if the effect (tested) allele in GWAS has increase or decrease risk of phenotype. And r2 does not change even ref/alt alleles in reference panel are flipped.

So why do I have to flip the sign of Z score if effect/non_effect alleles are opposite in reference panel?

Best, Kyoko

gkichaev commented 7 years ago

Hi Kyoko, The method relies on pearson correlations (r), not the squared correlation (r2), so the sign does matter.

In section 2 of the wiki this is described in detail.

https://github.com/gkichaev/PAINTOR_V3.0/wiki/2.-Input-Files-and-Formats

Good luck!

Kyoko-wtnb commented 7 years ago

Thank you for the quick response!!