R: Microsatellites genotypes of 237 cats from 17 colonies of...

nancycats {adegenet} | R Documentation

## Microsatellites genotypes of 237 cats from 17 colonies of Nancy (France)

### Description

This data set gives the genotypes of 237 cats (Felis catus L.) for 9 microsatellites markers. The individuals are divided into 17 colonies whose spatial coordinates are also provided.

### Format

`nancycats` is a genind object with spatial coordinates of the colonies as a supplementary components (@xy).

### Source

Dominique Pontier (UMR CNRS 5558, University Lyon1, France)

### References

Devillard, S.; Jombart, T. & Pontier, D. Disentangling spatial and genetic structure of stray cat (Felis catus L.) colonies in urban habitat using: not all colonies are equal. submitted to Molecular Ecology

### Examples

    ## Not run:
    data(nancycats)
    nancycats

    # summary's results are stored in x
    x <- summary(nancycats)

    # some useful graphics
    barplot(x$loc.n.all,ylab="Alleles numbers",main="Alleles numbers
    per locus")

    plot(x$pop.eff,x$pop.nall,type="n",xlab="Sample size",ylab="Number of alleles")
    text(x$pop.eff,y=x$pop.nall,lab=names(x$pop.nall))

    par(las=3)
    barplot(table(nancycats@pop),ylab="Number of genotypes",main="Number of genotypes per colony")

    # are cats structured among colonies ?
    if(require(hierfstat)){

    gtest <- gstat.randtest(nancycats,nsim=99)
    gtest
    plot(gtest)

    dat <- genind2hierfstat(nancycats)

    Fstat <- varcomp.glob(dat$pop,dat[,-1])
    Fstat
    }

    ## End(Not run)

[Package adegenet version 2.1.4 Index]