microsatt {ade4}R Documentation

Genetic Relationships between cattle breeds with microsatellites

Description

This data set gives genetic relationships between cattle breeds with microsatellites.

Usage

data(microsatt)

Format

microsatt is a list of 4 components.

tab
contains the allelic frequencies for 18 cattle breeds (Taurine or Zebu,French or African) and 9 microsatellites.
loci.names
is a vector of the names of loci.
loci.eff
is a vector of the number of alleles per locus.
alleles.names
is a vector of the names of alleles.

Source

Extract of data prepared by D. Lalo\"e ugendla@dga2.jouy.inra.fr from data used in:

Moazami-Goudarzi, K., D. Lalo\"e, J. P. Furet, and F. Grosclaude (1997) Analysis of genetic relationships between 10 cattle breeds with 17 microsatellites. Animal Genetics, 28, 338–345.

Souvenir Zafindrajaona, P.,Zeuh V. ,Moazami-Goudarzi K., Lalo\"e D., Bourzat D., Idriss A., and Grosclaude F. (1999) Etude du statut phylogénétique du bovin Kouri du lac Tchad à l'aide de marqueurs moléculaires. Revue d'Elevage et de Médecine Vétérinaire des pays Tropicaux, 55, 155–162.

Moazami-Goudarzi, K., Belemsaga D. M. A., Ceriotti G., Lalo\"e D. , Fagbohoun F., Kouagou N. T., Sidibé I., Codjia V., Crimella M. C., Grosclaude F. and Touré S. M. (2001)
Caractérisation de la race bovine Somba à l'aide de marqueurs moléculaires. Revue d'Elevage et de Médecine Vétérinaire des pays Tropicaux, 54, 1–10.

References

See a data description at http://pbil.univ-lyon1.fr/R/pps/pps055.pdf (in French).

Examples

## Not run: 
data(microsatt)
fac <- factor(rep(microsatt$loci.names, microsatt$loci.eff))
w <- dudi.coa(data.frame(t(microsatt$tab)), scann = FALSE)
wit <- within(w, fac, scann = FALSE)
microsatt.ktab <- ktab.within(wit)

plot(sepan(microsatt.ktab)) # 9 separated correspondence analyses
plot(mcoa(microsatt.ktab, scan = FALSE))
plot(mfa(microsatt.ktab, scan = FALSE))
plot(statis(microsatt.ktab, scan = FALSE))

## End(Not run)

Worked out examples


> library(ade4)
> ### Name: microsatt
> ### Title: Genetic Relationships between cattle breeds with microsatellites
> ### Aliases: microsatt
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(microsatt)
> fac <- factor(rep(microsatt$loci.names, microsatt$loci.eff))
> w <- dudi.coa(data.frame(t(microsatt$tab)), scann = FALSE)
> wit <- within(w, fac, scann = FALSE)
> microsatt.ktab <- ktab.within(wit)
> 
> plot(sepan(microsatt.ktab)) # 9 separated correspondence analyses
> plot(mcoa(microsatt.ktab, scan = FALSE))
> plot(mfa(microsatt.ktab, scan = FALSE))
> plot(statis(microsatt.ktab, scan = FALSE))
> 
> 
> 
> 

[Package ade4 Index]