I have binary data (0,1) from molecular markers amplification for 79 genotypes with 60 markers recorded. My data has NAs which i omitted when calculating the distance dist(). Now i am bit confused which R commands i can apply to detect my AMOVA analysis. I have gone through several websites and papers but i became more confused especially that the function (structure) doesn't work and every time i insert this command (amova(samples, dist(samples), str(samples)) gave me error! *samples are data frame and NAs are excluded from it. Where is the mistake then
I usually use the R package poppr when performing an AMOVA. Based on your script, I don't believe that is the function you are using. Poppr is built to handle the type of data you have, although I think the issue is selecting the proper genetic distance measure given the nature of your data. The authors also developed a nice tutorial.
http://grunwaldlab.github.io/Population_Genetics_in_R/AMOVA.html
You can try the GenAlex software for AMOVA. It is easy to use and user friendly both for binary and codominant data.
Dear Justin and Ioannis,
Thanks so much for your recommendations. I shall try both ways then.
Regards
Ioannis Ganopoulos
Can you please suggest/share the file format if we have to include both binary and codominant data for the analysis? That would be great help.
Thanks
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