DAPC Error

[Martin Boys]

Dear All

I am in dire need of your assistance with the following error I am encouraging with the DAPC analysis on RStudio. My research is based on 10 SSR loci across 3 populations with a total sample size of 55 individuals and of 1 stratum, pop. 

Kindly see below the scripts I run in bold and the outputs which eventually lead to the error. I followed the example of the primer, "Population genetics and genomics" by Kamvar, Everhart and Grunwald.

>library(adegenet)

>martin22

This is a genclone object

-------------------------

Genotype information:

 

    4 original multilocus genotypes

   55 haploid individuals

   10 codominant loci

 

Population information:

 

    1 stratum - Pop

    3 populations defined - Hybrid, Heirloom, Grape

>pop(martin22)<-martin22$other$epid

>dapc.martin22<-dapc(martin22,var.contrib=TRUE,scale=FALSE,n.pca=10,n.da=nPop(martin22)-1)

Error in dapc.genind(martin22, var.contrib = TRUE, scale = FALSE, n.pca = 10,  :

  x does not include pre-defined populations, and `pop' is not provided

>pop(martin)

NULL    

I understand that it has to do with the population which when I run results in the output, "NULL". However, the populations were defined as was seen in the output of the second script above. Any ideas on how I can bypass this error?

I thank you all in advance for your time to look at this email and for your inputs.

Best regards

Martin 

[Zhian Kamvar]

This line is removing your population. “epid” was a column from the tutorial. It likely does not exist in your data. Remove this line and rerun your analysis from the beginning:

>pop(martin22)<-martin22$other$epid

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[Martin Boys]

Thanks for the feedback. I only noticed that afterwards. Thank you so much

Regards

Martin