adegenet (version 2.1.10)

makefreq: Compute allelic frequencies

Description

The function makefreq is a generic to compute allele frequencies. These can be derived for genind or genpop objects. In the case of genind objects, data are kept at the individual level, but standardised so that allele frequencies sum up to 1.

Usage

makefreq(x, ...)
# S4 method for genind
makefreq(x, quiet = FALSE, missing = NA, truenames = TRUE, ...)
# S4 method for genpop
makefreq(x, quiet = FALSE, missing = NA, truenames = TRUE, ...)

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

Arguments

x

a genind or genpop object.

...

further arguments (curently unused)

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

deprecated; there for backward compatibility

Author

Thibaut Jombart

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.

Note that this function is now a simple wrapper for the accessor tab.

See Also

genpop

Examples

if (FALSE) {
data(microbov)
obj1 <- microbov
obj2 <- genind2genpop(obj1)

# perform a correspondance analysis on counts data
Xcount <- tab(obj2, NA.method="zero")
ca1 <- dudi.coa(Xcount,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
Xfreq <- makefreq(obj2, missing="mean")
Xfreq <- tab(obj2, NA.method="mean") # equivalent to line above
pca1 <- dudi.pca(Xfreq,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")
}