Dear Thibaut and Adegenet users,<br><br>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'.<br>
<br>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?<br>
Shall I create dummies individuals in 'pop1' and 'pop2' having the private alleles of 'popx'?<br><br>Hereafter is a reduced data set to illustrate the problem:<br>indiv pop L1 L2 L3<br>
Indiv1 pop1 222224 232224 120122<br>
Indiv2 pop1 222226 232226 118120<br>
Indiv3 pop1 222222 232232 120120<br>
Indiv4 pop1 222224 232224 124124<br>
Indiv5 pop2 224224 224224 122122<br>
Indiv6 pop2 224224 224224 124124<br>
Indiv7 pop2 224226 224226 120120<br>
Indiv8 pop2 222224 232224 122124<br>
Indiv9 popx 220222 220232 116118<br>
Indiv10 popx 222224 232224 118120<br>
Indiv11 popx 222226 232226 120120<br>
Indiv12 popx 224224 224224 124124<br><br><br><blockquote>geno<-read.table("three-pop.txt",h=T)<br><br>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])<br>
<br>trial@pop.names<br>split<- seppop(trial)<br><br>pop12 <- repool(split$pop1, split$pop2)<br><br>pop12 @all.names<br>split$popx@all.names<br></blockquote><br>In this case, 'pop12' has 10 columns of '@tab' while 'split$popx' has 13 columns of '@tab'.<br>
<br>Would anyone have a solution or any advice?<br><br>Thanks for your help,<br><br>Sébastien.<br><br clear="all">