R package PopGenome : error with introgression.stats function
Entering edit mode
13 months ago

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 :

[1] "Marpal"
[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!

PopGenome R • 311 views

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