[adegenet-forum] Importing Z (X) linked data?

[Jombart, Thibaut]

Hi there,

if you have a mixture of haploid/diploid genotypes, then you'd need to recode all as diploid, and then convert the data to genind (e.g. using df2genind). Note that the allele frequencies at a population level will be wrong. But individual-level multivariate analyses (PCA, PCoA, DAPC etc) will be OK

Cheers
Thibaut
________________________________________
From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Jeffrey DaCosta [dacostaj at bu.edu]
Sent: 04 July 2014 00:08
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] Importing Z (X) linked data?

I have a structure file for putative Z-linked loci for a set of birds. Since females are the heterogametic sex, they are coded as hemizygous (one allele and one “-9”) whereas males are diploid. The read.structure function seems to ignore females, I’m guessing because each female has a missing allele for all loci. I can recode all individuals as haploid and use df2genind, but does anyone have a different/better solution for getting these data into adegenet for a DAPC?

Thanks for any input,
-Jeff