R: Seasonal influenza (H3N2) HA segment data

H3N2 {adegenet} | R Documentation

## Seasonal influenza (H3N2) HA segment data

### Description

The dataset `H3N2` consists of 1903 strains of seasonal influenza (H3N2) distributed worldwide, and typed at 125 SNPs located in the hemagglutinin (HA) segment. It is stored as an R object with class genind and can be accessed as usual using `data(H3N2)` (see example). These data were gathered from DNA sequences available from Genbank (http://www.ncbi.nlm.nih.gov/Genbank/).

### Format

`H3N2` is a genind object with several data frame as supplementary components (`H3N2@other) slort`, which contains the following items:

x

  a `data.frame` containing miscellaneous annotations of the sequences.

xy

  a matrix with two columns indicating the geographic coordinates of the strains, as longitudes and latitudes.

epid

  a character vector indicating the epidemic of the strains.

### Details

The data file `usflu.fasta` is a toy dataset also gathered from Genbank, consisting of the aligned sequences of 80 seasonal influenza isolates (HA segment) sampled in the US, in `fasta` format. This file is installed alongside the package; the path to this file is automatically determined by R using `system.file` (see example in this manpage and in ?fasta2genlight) as well.

### Source

This dataset was prepared by Thibaut Jombart (t.jombart@imperia.ac.uk), 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

    ## Not run:
    #### H3N2 ####
    ## 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, posi.da="topleft", cstar=FALSE, cex=2, pch=17:22,
    solid=.5, bg="white")

    #### usflu.fasta ####
    myPath <- system.file("files/usflu.fasta",package="adegenet")
    myPath

    ## extract SNPs from alignments using fasta2genlight
    ## see ?fasta2genlight for more details
    obj <- fasta2genlight(myPath, chunk=10) # process 10 sequences at a time
    obj

    ## End(Not run)

[Package adegenet version 2.1.4 Index]