poppr and adegenet - DAPC for DArT

[u110...@umail.usq.edu.au]

Hello,

I am new to R and learning "poppr" and "adegenet" in R package for my data analysis. While performing the following codes/commands for DAPC analysis for my data set, I came across this error message. My data set is haploid and consisting of dominant markers. Since I could not rectify the error with my data set, herewith I attached a sub-sample of my data set for your reference. 

I would be grateful to you if you could help me to figure out the error and perform my analysis. 

Thank you.

Sincerely,

Buddhika   

Command 

library("adegenet")

genrr1 <- read.genalex("C:/Users/u1107303/Desktop/genrr1.csv")

splitStrata(genrr1) <- ~location/form

genrr1

pop(genrr1) <- genrr1$other$epid

dapc.genrr1 <- dapc(genrr1, var.contrib = TRUE, scale = FALSE, n.pca = 30, n.da = nPop(genrr1) - 1)

scatter(dapc.genrr1, cell = 0, pch = 18:23, cstar = 0, mstree = TRUE, lwd = 2, lty = 2)

Message 

  library("adegenet")

> genrr1 <- read.genalex("C:/Users/u1107303/Desktop/genrr1.csv")

Warning in read.genalex("C:/Users/u1107303/Desktop/genrr1.csv") :

  

 I found duplicate column names in your data.

 They are being renamed:

 col 2918: 28946770 -> 28946770_1

 col 3399: 36349730 -> 36349730_1

 col 3819: 28945475 -> 28945475_1

 col 3870: 28949490 -> 28949490_1

 col 4112: 36350716 -> 36350716_1

 col 4672: 36351425 -> 36351425_1

Warning message:

In df2genind(gena, ind.names = ind.vec, pop = pop.vec, ploidy = ploidy,  :

  non-polymorphic marker(s) deleted

> splitStrata(genrr1) <- ~location/form

> genrr1

This is a genclone object

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

Genotype information:

     89 original multilocus genotypes 

     89 diploid individuals

   7314 dominant loci

Population information:

      2 strata - location, form

     13 populations defined - pop1_t, pop2_t, pop2_m, ..., pop7_t, pop7_m, pop8_t

> pop(genrr1) <- genrr1$other$epid

> dapc.genrr1 <- dapc(genrr1, var.contrib = TRUE, scale = FALSE, n.pca = 30, n.da = nPop(genrr1) - 1)

Error in dapc.genind(genrr1, var.contrib = TRUE, scale = FALSE, n.pca = 30,  : 

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

[Buddhika Amarasinghe Dahanayaka]

Hello Dr. Kamvar,

I am contacting you regarding the same data set I sent you previously. I removed some of my loci and was doing some analyses. I did not change anything except the number of markers in my data set. Now I have 7156 markers and when I run the following commands it says I have 7155 markers and the data set is codominant. But it is a dominant data set. Previously I did not have this problem. 

I would be grateful if you could help me with this issue. 

Thank you.

Sincerely,

Buddhika 

commands

library(poppr)

genrr1 <- read.genalex("C:/Users/u1107303/Desktop/genrr1.csv")

genrr1

Observation in Console 

Genotype information:

     89 original multilocus genotypes

     89 haploid individuals
   7155 codominant loci

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[Zhian Kamvar]

Hello,

Two things:

1. It’s difficult to diagnose without knowing what the data looks like, but I suspect that the reason your data mentions one fewer marker is that one of your markers was invariant and was dropped (you would have gotten a warning about that)

2. You mentioned in your earlier email that you have SNP data, which are considered co-dominant as they do not necessarily have a strict binary state. 

Sent from my iPhone

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