[adegenet-forum] Structure-like membership plot

[Jombart, Thibaut]

Hello,

normally the results should be the same, although clusters found by find.clusters will likely differ from one run to another. E.g. cluster 1 will become 4 etc.

Are you sure this is not the source of the differences? If you want to check that the data are identical, you can compare the matrices of individual frequencies:
all.equal(x1$tab,x2$tab)

where x1 and x2 are genind imported with different methods.

I would need at least a head(tab) to check that df2genind is well used.

Cheers

Thibaut
________________________________
From: Huang,Cheng-Hua [arhua at ufl.edu]
Sent: 04 July 2011 16:09
To: Jombart, Thibaut; adegenet-forum at r-forge.wu-wien.ac.at
Cc: arhuahuang at gmail.com
Subject: RE: [adegenet-forum] Structure-like membership plot

Dear Thibaut,

Thank you for your help. I used the way you advised me to convert the Strucutre file of my haploid data set into a genind object as follow:

dat <- read.table("structure.str", sep="\t",head=TRUE)
x <- df2genind(dat[,-(1:2)], ploidy=1, pop=dat[,2], ind.names=dat[,1])
and then

###
find.cluster(x)
dapc(x)…
However, the membership plot derived from this Structure file (showing admixture individuals) was different those obtained from using import2genind to convert Genepop and Fstat files of the same data set where data were coded as a pseudo-diploid (no admixture individuals). Did I convert my structure data set wrong? Or, I should trust results from Genepop and Fstat data sets? Thank you.
Regards,
Arhau

From: Jombart, Thibaut [mailto:t.jombart at imperial.ac.uk]
Sent: Monday, July 04, 2011 9:30 AM
To: Huang,Cheng-Hua; adegenet-forum at r-forge.wu-wien.ac.at
Cc: arhuahuang at gmail.com
Subject: RE: [adegenet-forum] Structure-like membership plot

Dear Arhua,

read.structure is only meant for diploid data - will add a warning on this point in the doc for 1.3-1.

So your analysis based on read.structure here is wrong. The other analyses are surely OK. Otherwise use read.table/read.csv to read your structure data into R as a data.frame, and then df2genind with the proper arguments to convert the data into a genind object.

Best

Thibaut

--
######################################
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jombart at imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Cheng-Hua Huang [arhua at ufl.edu]
Sent: 01 July 2011 17:10
To: adegenet-forum at r-forge.wu-wien.ac.at
Cc: arhuahuang at gmail.com
Subject: [adegenet-forum] Structure-like membership plot
Dear adegent users and Thibaut,
I would like to ask questions about using DAPC. I have used import2genind and df2genind for importing Structure, Genepop, and Fstat files of the same data set to find clusters and to plot Struture-like membership information. Since I was working on a haploid, asexual fungus collected from three regions, I coded data sets as a pseudo-diploid for Genepop and Fstat files but used the original haploid data set for the Structure format. Even though I got K=3 for biological interpretation based on BIC, the membership plot derived from the Structure input file was different from those obtained from the other two file formats. The result using the Structure input format showed many admixture individuals, but the other two input files did not exhibit any admixture individuals (all with membership probability = 1). The latter makes sense to me because the fungus is asexual and genotype flow plays a main role in shaping population structure. Moreover, recombination is not possible for this fungus. Thus, admixture individuals may not occur. What caused this difference between these input files? How do I interpret these results? Thank you for your help.
Regards,
Arhua


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