humDNAm: human mitochondrial DNA restriction data

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

This data set gives the frequencies of haplotypes of mitochondrial DNA restriction data in ten populations all over the world.
It gives also distances among the haplotypes.

Usage

data(humDNAm)

Format

humDNAm is a list of 3 components.

distances

is an object of class dist with 56 haplotypes. These distances are computed by counting the number of differences in restriction sites between two haplotypes.

samples

is a data frame with 56 haplotypes, 10 abundance variables (populations). These variables give the haplotype abundance in a given population.

structures

is a data frame with 10 populations, 1 variable (classification). This variable gives the name of the continent in which a given population is located.

Source

Excoffier, L., Smouse, P.E. and Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479–491.

Examples

data(humDNAm)
dpcoahum <- dpcoa(data.frame(t(humDNAm$samples)), 
    sqrt(humDNAm$distances), scan = FALSE, nf = 2)
plot(dpcoahum)

Example output

ade4 documentation built on May 2, 2019, 5:50 p.m.