[adegenet-forum] Using mtDNA haplogroup data to perform DAPC and sPCA

Guillermo Reales Monteagudo greales at ucm.es
Wed May 21 10:29:25 CEST 2014


I've just started to learn about the package and tried to use it on my own
data, but I'm still having some issues which I suspect might be related to
data input. I contact you to check whether I'm in the good direction or not.

My initial data are haplogroup frequencies in several (63) populations
(total n = 944), so I for genind object construction I decided to treat
these (9) haplogroups as haploid alleles of a single marker (i.e. 1 locus,
9 alleles in this case). First I converted my frequencies to absolute
frequencies in each population and then I designed a function to retrieve a
matrix with individual genotypes to fit a genind structure - 944-row matrix
with ones and zeroes corresponding to each individual haplogroup.
Plus, I included a factor assigning these individuals to each population,
and a proper xy list including UTM coordinates for each individual.
After constructing my genind and genpop objects I started performing some
DAPC and sPCA analyses, yet I still don't know whether I can trust my
results or not, as I haven't found any example handling such input data
type to compare to.
Any suggestion for improvement?
Thank you all in advance.

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