Hi all, I am trying to plot manhattan plot from my GWAS object from rrBLUP. rrBLUP does display Manhattan plots with significant threshold line using qvalue package from Bioconductor. I am instead trying to make my own custom Manhattan plot (using qqman R package) since it is a lot customizable with significant threshold line. For that I am using the same qvalue package as follows:
qobj<- qvalue (p, fdr.level = 0.05)
The qobj has following components:
 "call" "pi0" "qvalues" "pvalues" "lfdr" "fdr.level"
 "significant" "pi0.lambda" "lambda" "pi0.smooth"
I can use "significant" component for downstream analysis. But how can I get that single significant threshold value to plot in my custom Manhattan plot?
Your help is much appreciated.