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KosukeHamazaki / RAINBOWR

Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS and multi-kernel mixed model)
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007663
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CalcThreshold function often return NA #2

Closed flystar233 closed 6 months ago

flystar233 commented 4 years ago

First of all, thank you very much for your work. It returns NA when I use CalcThreshold to calculate the GWAS threshold. The P value of most of my results is not very significant, as shown below。Do you have any suggestions? QQ图片20200821110450

KosukeHamazaki commented 4 years ago

Thank you for your question.

If you use the Benjamini-Hochberg method for multiple comparison correction (method = "BH" in CalcThreshold function), the GWAS threshold cannot be calculated when there is no significant peak, such as your result. Thus, I think it is no problem that the threshold for your results was NA. If you really want to calculate the GWAS threshold, you can try the Bonferroni method by using method = "Bonf" in CalcThreshold function.