I am using Rehh package for identification of positively selected genes from our study. I am using the following script but confused with right reference.
ies2xpehh( scan_pop1, scan_pop2, popname1 = NA, popname2 = NA, min_nhaplo = NA, standardize = TRUE, include_freq = FALSE, p.side = NA, p.adjust.method = "none", verbose = TRUE )
Here, which population is positively selected xpehh score. Popname1 or popname2?
Please share your experience.