[adegenet-forum] Genotypes assignment to clusters

[Sébastien Puechmaille]

Dear Thibaut and Adegenet users,

I have a data set with 3 groups of samples (see below), 2 with samples of
known origin (pop1 and pop2) and one (popx) with samples that I would like
to assign to one of the 2 known populations (pop1 or pop2). For this, I want
to run a DAPC with 'pop1' and 'pop2' data set and then, assign individuals
from 'popx' to either 'pop1' or 'pop2'.

However, individuals from the group to be assigned have some private alleles
that are neither in 'pop1' nor in 'pop2' and therefore, the assignment
cannot work. What would be the best solution to get around this problem?
Shall I create dummies individuals in 'pop1' and 'pop2' having the private
alleles of 'popx'?

Hereafter is a reduced data set to illustrate the problem:
indiv    pop    L1    L2    L3
Indiv1    pop1    222224    232224    120122
Indiv2    pop1    222226    232226    118120
Indiv3    pop1    222222    232232    120120
Indiv4    pop1    222224    232224    124124
Indiv5    pop2    224224    224224    122122
Indiv6    pop2    224224    224224    124124
Indiv7    pop2    224226    224226    120120
Indiv8    pop2    222224    232224    122124
Indiv9    popx    220222    220232    116118
Indiv10    popx    222224    232224    118120
Indiv11    popx    222226    232226    120120
Indiv12    popx    224224    224224    124124


geno<-read.table("three-pop.txt",h=T)

trial<-df2genind(geno[,3:5],missing=NA,ploidy=2,sep=NULL,ncode=6,ind.names=geno[,1],
loc.names=colnames(geno[1,3:5]),pop=geno[,2])

trial at pop.names
split<- seppop(trial)

pop12 <- repool(split$pop1, split$pop2)

pop12 @all.names
split$popx at all.names


In this case, 'pop12' has 10 columns of '@tab' while 'split$popx' has 13
columns of '@tab'.

Would anyone have a solution or any advice?

Thanks for your help,

Sébastien.
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