[adegenet-forum] seploc resets ploidy information to diploid

[Zhian Kamvar]

Hello,

I was working on some analyses dealing with polyploids, and I noticed that
seploc resets the ploidy information of each locus to diploid, regardless
of initial ploidy. For a simplified example, here's your example from the
adegenet-basics.pdf:

> temp <- lapply(1:30, function(i) sample(1:9, 4, replace=TRUE))
> > temp <- sapply(temp, paste, collapse="")
> > temp <- matrix(temp, nrow=10, dimnames=list(paste("ind",1:10),
> paste("loc",1:3)))
> > obj <- df2genind(temp, ploidy=4, sep="")
>
> objloc <- seploc(obj)
> > sapply(objloc, ploidy)
> loc 1 loc 2 loc 3
>     2     2     2
> > ploidy(obj)
> [1] 4
>

I went into the adegent source code and found where the trouble was. It's
on line 99 of "handling.R":

kX <- lapply(kX, genind, pop=x at pop, prevcall=prevcall)
>
To preserve ploidy, I think this line should be:

kX <- lapply(kX, genind, pop=x at pop, prevcall=prevcall, ploidy = x at ploidy)
>

Can this be implemented in the next version of adegenet?

Thanks,
Zhian N. Kamvar
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