[adegenet-forum] RAPD data

Jombart, Thibaut t.jombart at imperial.ac.uk
Wed Feb 29 11:31:57 CET 2012


Assuming your RAPD data are dominant, it is by definition impossible to distinguish heterozygotes from homozygotes, or to compute allele frequencies (hence no Fst, no HW test). You can still derive a similarity matrix using propShared. Note that the output will no longer be the proportion of shared alleles, but the proportion of allele presence common to pairs of sequences.



From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Ayman Sabry [amsabry at gmail.com]
Sent: 29 February 2012 10:05
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] RAPD data

I have RAPD data, I like to estimate heterozyosity, Fst , hw.test,  as well as similarity matrix
My question is,
could I do these tests using adegenet or pegas on RAPD data?
Thanks in advance

Ayman Sabry, Ph.D.
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