Clone correction, AMOVA and DAPC

[Buddhika Amarasinghe Dahanayaka]

Hi all,

I am working on a haploid population and my markers dominant makers. I need to clone correct my population as I know there are clones in my population. 

I cannot do the clone correction according to the tutorial given in "population genetics and genomics in R" as I have only one stratum (location). Also, I uploaded my data file using the following command and it says that my population is diploid but which is not.

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

char

I tried to run "Splitstrata/setpop" commands and do AMOVA, but it says that I do not have "location" in my data frame. My aim was to check whether there is a molecular variance of my population according to the sampling location.  I tried to do DAPC also but it also did not work. 

I would be grateful to you if you could assist me with these issues. I have attached a subset of my data for your reference. 

Many thanks.

Sincerely,

Buddhika     

[Buddhika Amarasinghe Dahanayaka]

Hi,

I have an issue with clone correction. I have around 4000 markers generated from DArTseq. This time my population size is 403 and I am supposed to get clones in this population. However, when I ran the following codes it gives me the same number (403) of MLGs (Says no clones). I was wondering whether this is due to the missing data and errors in genotyping. I did not contract the data set as I wanted to check the clones. But then I tried contracting the data set and finding the clones, then it gives me the contracted number of genotypes as clones. 

 pop37_cc <- clonecorrect(pop37, strata = 1, combine = FALSE, keep = 1). 

I have only one statra as you can see in the image. 

 

I would be grateful if you have any suggestion.

Thanks in advance :)

Buddhika

[Zhian N. Kamvar]

Hello Buddhika,

This situation was the motivation for the `mlg.filter()` function, which we introduced in 2015: https://www.frontiersin.org/articles/10.3389/fgene.2015.00208/full#h3 You can define a distance threshold to account for genotyping errors using this function. This tutorial can help: https://grunwaldlab.github.io/poppr/articles/mlg.html#multilocus-genotype-flavors-1

Best,

Zhian

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