Permutation Analysis for SNP Significance?

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Zachary Tatom

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Apr 1, 2021, 8:47:18 PM4/1/21

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Hi all,

I'm fairly new to QTL analysis. I've been able to do SNP analysis and use the drop_hilit argument while plotting, but as far as I can tell it's only possible to hilight SNPs that fall within an arbitrary LOD drop value of the top SNP.

Is there any way to run a permutation analysis to identify significance thresholds for SNP LOD scores (similar to `scan1perm()`)?

Thanks,

Zack

Karl Broman

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Apr 1, 2021, 10:57:00 PM4/1/21

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I’ve not yet implemented a permutation analysis for the snp association scan. It’s on my “to do” list (https://github.com/rqtl/qtl2/issues/58).

karl

Zachary Tatom

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Apr 2, 2021, 2:28:31 PM4/2/21

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Thanks! If there's any way to aid in its implementation, please let me know.

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