I ran Tassel3 and I filtered results with p-value not more than 0.05. This way, it is ok to draw a Manhattan plot. However, for a QQ-plot there is a problem.
Say I have 40 thousands SNPs, after filtering, about 1,800 SNPs were kept in the output file. Now how do I draw QQ-plot because of partial p-values?
ppoints only generate points within (0,1). I think the resulting points
should be in the filtered range (0,0.05) with the same number (1,800) too.
runif can do the trick, but it is random, each time it generates different
results. I think this would affect the QQ-plot line.
I figured out three ways to solve it but I am not sure if it is right. Hope you guys can give some advices.
the following are three methods:
ppoints(1800*100/0.05, a=0.05), then I only get the former 1/20 results.
ppoints(40k), and use those p-values below 0.05 in plotting.