On 23 Feb 2015, at 8:52 pm, Benjamin Alric <benjamin.alric at imbe.fr> wrote:
Dear all,
I would like simulated hybridization between two population to assess
the power of admixture analysis (STRUCTURE).
I built two subsamples consisting of 30 indivudals showing the highest q
values for the cluster1 or cluster2 of previously STRUCTURE analysis.
From these two subsamples I would like simulated hybridization (using
hybridize function of the adegenet R package) to assess the power of
admixture analysis.
For each population, genotype were determined through 8 microsatellite
loci for wichi one allele is code by a character string of 3 numbers.
Here you are the command:
Dg<-import2genind("B_Dg.gtx",package="adegenet")
Dl<-import2genind("B_Dl.gtx",package="adegenet")
Dg<- #####################
### Genind object ###
#####################
- genotypes of individuals -
S4 class: genind
@call: read.genetix(file = file, missing = missing, quiet = quiet)
@tab: 30 x 33 matrix of genotypes
@ind.names: vector of 30 individual names
@loc.names: vector of 8 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the 33 columns of @tab
@all.names: list of 8 components yielding allele names for each locus
@ploidy: 2
@type: codom
Optional contents:
@pop: factor giving the population of each individual
@pop.names: factor giving the population of each individual
@other: - empty -
Dl<-#####################
### Genind object ###
#####################
- genotypes of individuals -
S4 class: genind
@call: read.genetix(file = file, missing = missing, quiet = quiet)
@tab: 30 x 33 matrix of genotypes
@ind.names: vector of 30 individual names
@loc.names: vector of 8 locus names
@loc.nall: number of alleles per locus
@loc.fac: locus factor for the 33 columns of @tab
@all.names: list of 8 components yielding allele names for each locus
@ploidy: 2
@type: codom
Optional contents:
@pop: factor giving the population of each individual
@pop.names: factor giving the population of each individual
@other: - empty -
hybrdis<-hybridize(Dg,Dl,n=100,pop="Hybrids")
g1<-genind2df(hybrids)
g1<-
pop 10_14 Dp512 SwiD1 SwiD10
SwiD12 SwiD14 SwiD15 SwiD5
h001 Hybrids 226226 129 131143 194201 112119
181185 093098 161161165
h002 Hybrids 220226 129 126138 200201 112 175
181181 089098 151153165
h003 Hybrids 220226 129 126134143 200 123123 185185
093098 153163165
h004 Hybrids 220226 129 126131 200201 119123
185185 093098 153153165
h005 Hybrids 220226 129 126136136 199 123123 181185
089098 153161165
h006 Hybrids 226226 129129 136136 194 112112 181181
089098 153161165
h007 Hybrids 220226 129133 134143 194 119 175
181185 093 151153163165
....
We would expect to see two allele for each locus but it is not the case
for all microsatellite loci.
Somebody know why and where does the problem?
I checked the example dataset "microbov" for hybridize function, and I
see that temp$Salers and temp$Zebu (used to perform simulated
hybridization with hybridize function) presented the same count of
alleles at each locus.
When I check now my two datasets, I see that there are not the same
number of allele between the two populations. such a difference in the
number of allele between the two population could be the origne of the
problem...
Dg at all.names
$L1
1 2 3
"220" "226" "231"
$L2
1 2 3
"125" "129" "133"
$L3
1 2 3 4 5 6
"126" "131" "134" "136" "138" "143"
Dl at all.names
$L1
1 2 3
"223" "226" "229"
$L2
1 2 3 4 5 6
"129" "133" "136" "137" "138" "139"
$L3
1 2 3 4 5 6 7
"118" "134" "136" "138" "145" "150" "152"
Thank in advence for your help.
Sincerely yours,
Benjamin ALRIC
--
--
Benjamin Alric,PhD
UMR 7263-CNRS / 237-IRD - Institut M?diterran?en de Biodiversit? et d'Ecologie (IMBE)
Equipe "Ecologie des Eaux Continentales"
Aix-Marseille Universit?, Facult? des Sciences, site de St J?r?me
52 Avenue Escadrille Normandie Ni?men
13397 Marseille cedex 20 - France
T?l: +33 (0)4 13 59 46 46