[adegenet-forum] adegenet

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu May 6 13:53:09 CEST 2010

Dear Farhad, 

please have a look at the adegenet tutorial for importing data (http://adegenet.r-forge.r-project.org/), it's all explained there.



From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] On Behalf Of farhad vahidi [smf.vahidi at gmail.com]
Sent: 05 May 2010 08:25
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] adegenet

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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