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.
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written
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tothepoint
1 answer
Hey devarora,
If you're still having this problem, check this github page https://speciationgenomics.github.io/haplotypes/ . It helped me out.
house_bac <- ies2xpehh(bac_scan, house_scan,
popname1 = "bactrianus", popname2 = "house",
include_freq = T)
ggplot(house_bac, aes(POSITION, XPEHH_bactrianus_house)) + geom_point()
"In this plot, highly negative values suggest selection in population 2 (house in this case) whereas positive values indicate selection in population 1. Alternatively, like with iHS, we could plot the log P values."
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