GAPIT p-value significance threshold

Question

[Clayton]

Hi all,

I have GWAS results for several traits in barley. However, I have been told that 0.05 significance threshold may be too stringent for plants.

Does anyone know how to adjust the significance threshold in GAPIT? Specifically, is the default setting 0.05 divided by the # of markers? Therefore, adjusting "cutoff = 0.05" in the GAPIT function to "cutoff = 1" will give me threshold of 1 divided by the # markers?

Thanks for reading.

[ginellegrenier]

Hi, I was wondering if you have found a solution to this? Thanks!