adegenet (version 1.2-7)

H3N2: Seasonal influenza (H3N2) HA segment data

Description

This dataset consists of 1903 strains of seasonal influenza (H3N2) distributed worldwide, and typed at 125 SNPs located in the hemagglutinin (HA) segment. These data were gathered from DNA sequences available from Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).

Usage

data(H3N2)

encoding

UTF-8

source

This dataset was prepared by Thibaut Jombart ([e-mail]), from annotated sequences available on Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).

References

Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Submitted to BMC genetics.

Examples

## LOAD DATA
data(H3N2)
H3N2

## set population to yearly epidemics
pop(H3N2) <- factor(H3N2$other$epid)



## PERFORM DAPC - USE POPULATIONS AS CLUSTERS
## to reproduce exactly analyses from the paper, use "n.pca=1000"
dapc1 <- dapc(H3N2, all.contrib=TRUE, scale=FALSE, n.pca=150, n.da=5)
dapc1

## (see ?dapc for details about the output)


## SCREEPLOT OF EIGENVALUES
barplot(dapc1$eig, main="H3N2 - DAPC eigenvalues")


## SCATTERPLOT (axes 1-2)
scatter(dapc1, ratio=.2)