[adegenet-forum] adegenet

farhad vahidi smf.vahidi at gmail.com
Wed May 5 09:25:07 CEST 2010

Dear Jombart,
Hi. as i wrote you before, I have 10 populations and 18 microsatellite
markers. I want to perform single- marker PCA and global PCA using adegenet
package. for reading and then importing my data in genind I peform the
following lines:
sheep<- read.loci("D:/farhad.txt", header=TRUE, loci.sep= "\t" , allele.sep
= "/", row.names=1)
df2genind(sheep, sep="/" )

 then i received the following results:

S4 class:  genind

@call: df2genind(X = sheep, sep = "/")

@tab:  411 x 249 matrix of genotypes

@ind.names: vector of  411 individual names

@loc.names: vector of  18 locus names

@loc.nall: number of alleles per locus

@loc.fac: locus factor for the  249 columns of @tab

@all.names: list of  18 components yielding allele names for each locus

@ploidy:  2

@type:  codom

Optionnal contents:

@pop:  - empty -

@pop.names:  - empty -

@other: - empty -

as you can see about @pop, @pop.names, these are empty. for example when I
perform sheep$loc.names and/or sheep$loc.nall i obtained NULL output.
would you please let me know my mistake here.
Best regards
Farhad Vahidi
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