[adegenet-forum] Grouping crossvalidation DAPC

[Florian Leplat]

Dear Adegenet user,


I was previously using adegenet package for genetic applications.

Since I started to use the DAPC function. The methods is very informative.
However there are some details that I would like to understand better.



The main objective of my use is to group a certain number of plant genotype
regarding to their genotypic background. Each genotype are homozygous lines.

I have no prerequisite information for any genotype. Therefore the main
idea is to attribute a “group number” for each of my plants.



I does work fine with a good comprehensiveness regarding to the information
that I have for each plants (origin, parents...)

However, one of the limitations that I face is the repeatability of the
grouping. If running several time, a certain number of plant will be
attributed to a different group. Is there a cross-validation procedure at
this step in order to look at the percentage of plant always grouped
together for each run ?



Furthermore, even if my grouping are quite consistent “group wise” from one
run to the other, the grouping number will change. Is there a way to solve
that (for instance give a group number to the founder genotype of our
population) ?



Then I have a second issue. After the first step which define my groups, I
would like to plot hybrids genotypes which should (could) be an admixture
between 2 groups. Therefore I cannot use them to build my groups as they
add some noise to the model. I wanted to use the procedure described in the
tutorial using supplementary individuals. I realized that it only works if
the supplementary individuals have already grouping information, however I
don’t have this information. Indeed I only want to see (mostly visually)
where the hybrids are positioned in relation to the other groups that I
previously defined. Is there a way to use the script to do that ?



Thanks in advance for your help.

Best regards.


*Flo*
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