how to make groups or strucuration of individuals in R?
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6.6 years ago

Hi to all Good Morning

I have 93 individuals with 395 SNPs genotype data with me and there is no population information available for those individuals. Now I would like group those individuals into certain groups based on their genetic similarity but not like dendrogram. I checked DAPC function in adegenet package in R but it requires population information. I think I can make grouping in structure software but it is time taking and I am new to it. is there any possibility to group my individuals into different groups in R? if yes I am requesting all to share your experience Thanks in advance With Kind Regards

R • 1.0k views
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What you want is called clustering and there are plenty of algorithms to do this, many of them available in R. Why don't you want to use hierarchical clustering ? With a relevant measure of similarity it often gives a good idea of the data structure, in your case, it would give you an idea of how the individuals tend to group and you could use this information for example to determine the number of clusters you want from another clustering algorithm.

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