makefreq {adegenet}R Documentation

Function to generate allelic frequencies

Description

The function makefreq generates a table of allelic frequencies from an object of class genpop.

Usage

makefreq(x,quiet=FALSE,missing=NA,truenames=TRUE)

Arguments

x an object of class genpop.
quiet logical stating whether a conversion message must be printed (TRUE,default) or not (FALSE).
missing treatment for missing values. Can be NA, 0 or "mean" (see details)
truenames a logical indicating whether true labels (as opposed to generic labels) should be used to name the output.

Details

There are 3 treatments for missing values:
- NA: kept as NA.
- 0: missing values are considered as zero. Recommended for a PCA on compositionnal data.
- "mean": missing values are given the mean frequency of the corresponding allele. Recommended for a centred PCA.

Value

Returns a list with the following components:

tab matrix of allelic frequencies (rows: populations; columns: alleles).
nobs number of observations (i.e. alleles) for each population x locus combinaison.
call the matched call

Author(s)

Thibaut Jombart jombart@biomserv.univ-lyon1.fr

See Also

genpop

Examples

data(microbov)
obj1 <- microbov

obj2 <- genind2genpop(obj1)

Xfreq <- makefreq(obj2,missing="mean")

if(require(ade4)){

# perform a correspondance analysis on counts data

Xcount <- genind2genpop(obj1,missing="chi2")
ca1 <- dudi.coa(as.data.frame(Xcount@tab),scannf=FALSE)
s.label(ca1$li,sub="Correspondance Analysis",csub=1.2)
add.scatter.eig(ca1$eig,nf=2,xax=1,yax=2,posi="topleft")

# perform a principal component analysis on frequency data
pca1 <- dudi.pca(Xfreq$tab,scale=FALSE,scannf=FALSE)
s.label(pca1$li,sub="Principal Component Analysis",csub=1.2)
add.scatter.eig(pca1$eig,nf=2,xax=1,yax=2,posi="top")
}

[Package adegenet version 1.2-2 Index]