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Jiacheng Miao edited this page Mar 14, 2023 · 8 revisions

GWAS summary statistics

Q. Whether the additive effect GWAS need to include GxE terms when used in PIGEON?

A. No, the additive effect GWAS does not require the inclusion of GxE terms. Therefore, you can use the summary statistics of almost all GWAS as input for PIGEON!

GWIS (SNPxE) summary statistics

Q. If the GWIS (SNPxE) analysis is performed without centering the environment, can I use this GWIS as input to PIGEON?

A. Yes, you can use the GWIS summary statistics with or without centering the environment. PIGEON only used the Z-score for SNPxE results, which is invariant to centering and standardization of the environment. The detailed proof can be found in the Lemma1 of the Supplementary Note in the PIGEON paper

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