Hi everyone,
I'm currently facing a problem while using the R package PopGenome. I'm trying to perform patterson D and df analyses on non overlapping sliding windows but I face an error regarding the outgroup needed to perform such analyses. I checked on the internet but didn't find an answer to my problem. Here is my code :
A <- c("Caz-A", "NILSC1", "NILSC11", "NILSC13", "NILSC16")
B <- c("Ale-A", "Ber-A", "Ber-B", "Ber-C", "Ber-D", "Ber-F", "Bid-A", "Bie-B", "Bie-C", "Bot-X", "Bul-A", "Bul-B", "Bul-C", "CA")
C <- c("NILSC12", "NILSC14", "NILSC17", "NILSC18", "NILSC20")
D <- "Marpal"
chr1 <- readData("VCF_chr1", format = "VCF", outgroup = D, populations = list(A,B,C))
chr1 <- introgression.stats(chr1, do.D = T, do.df = F, block.size = 500)
chr1_slide <- sliding.window.transform(chr1, width = 50000, jump = 50000, type = 2, start.pos = 1, end.pos = 30584173)
chr1_slide <- set.populations(chr1_slide, list(A,B,C))
chr1_slide <- set.outgroup(chr1_slide, new.outgroup = D)
chr1_slide <- introgression.stats(chr1_slide, do.D = T, do.df = T, do.RNDmin = F, block.size = 50)
It's actually working for the whole chromosome (chr1), but when I'm trying to do it on sliding windows (chr1_slide) I get the following error:
Error in calc_D(bial, populations, outgroup, keep.site.info) :
This statistic needs an outgroup ! (set.outgroup)
When I check for an outgroup in chr1_slide I get this so I don't understand why the function introgression.stats can't detect the outgroup :
print(chr1_slide@outgroup)
[1] "Marpal"
length(chr1_slide@outgroup)
[1] 1
If anyone have an idea about what is the cause of the error or how can I solve this I would be grateful.
It is my first post here, I hope it's understandable. Have a great day!
