[R] stats 'dist' euclidean distance calculation

[S Ellison]

> 3x3 subset used
>                          Locus1     Locus2         Locus3
> Samp1               GG           <NA>           GG
> Samp2               AG             CA              GA
> Samp3               AG             CA              GG
> 
> The euclidean distance function is defined as: sqrt(sum((x_i - y_i)^2)) My
> assumption was that the difference between x_i and y_i would be the number
> of allelic differences at each base pair site between samples. 

Base R does not share your assumption, which (from a general purpose stats point of view) would be a completely outlandish interpretation of the data. As far as base R is concerned, these are just arbitrary character strings represented (by default) as factors. Since factors are, internally, integers assigned (by default) in increasing lexical order to the levels present, if you apply dist() to factors constructed from allele data, you will usually get complete nonsense in genetic terms. 

You should probably look at something like dist.gene in the ape package: see
https://www.rdocumentation.org/packages/ape/versions/5.0/topics/dist.gene

S Ellison


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