[adegenet-forum] propShared problems

[Jombart, Thibaut]

Dear Tim, 

thanks for the file. I'll be looking into this when I'm back from holidays, at the beginning of September.

Meanwhile, you can try a kludge to solve your problem. Read your data into a data.frame, create a genind using df2genind, specifying that you have haploid data (this is the kludge), and then compute the proportion of common alleles using propShared.

Best regards

Thibaut.

________________________________________
From: Timothy Frasier [timothy.frasier at SMU.CA]
Sent: 16 August 2010 14:53
To: Jombart, Thibaut
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: [adegenet-forum] propShared problems

Dear Thibaut,

The .RData file is attached.  The command line used for creating the genind file is:

> ds1 <- read.structure("porpoise.str", n.ind=35, n.loc=9, onerowperind=T, col.lab=1, col.pop=0, col.others=0, row.marknames=0, missing=NA, ask=T, quiet=F)

Then,

> save(ds1, file="porpgenind.RData")

Again, the genind file seems to read it correctly as a diploid data set, but that seems to be lost when trying to use the propShared function.

Thanks again!

-Tim