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

In adegenet: Exploratory Analysis of Genetic and Genomic Data

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)

adegenet documentation built on Feb. 16, 2023, 6 p.m.