adegenet (version 1.0-0)

Auxiliary functions: Utilities functions for adegenet objects

Description

Theses functions are to be used with genind and genpop objects. truenames returns elements of the object with using true names (as opposed to generic labels) for individuals, markers, alleles, and population. The function seploc splits the table (x$tab) by marker, allowing separate analysis of markers.

Usage

truenames(x)
seploc(x,truenames=FALSE)

Arguments

x

a genind or genpop object.

truenames

a logical indicating whether generic labels (FALSE,default) or true names should be used (TRUE).

Value

• The function truenames returns a matrix similar to x$tab but with true labels. If x$pop exists, it returns a list with this matrix ($tab) and a population vector with true names ($pop). The function seploc applied to genind or genpop objects returns a list of matrices, one per marker.

Examples

data(microbov)
# restore true names
truenames(microbov)$tab[1:5,1:5]

# isolate each marker
obj <- seploc(microbov,truenames=TRUE)
names(obj)

# make a new object with INRA5
head(obj$INRA5)
inra5.gind <- as.genind(obj$INRA5)
inra5.gind

# perform tests only on this marker
if(require(genetics)){
hw.test <- HWE.test.genind(inra5.gind,pop=microbov$pop,res.type="matrix",permut=TRUE) 
hw.test
}

if(require(hierfstat)){
g.test <- gstat.randtest(inra5.gind,pop=microbov$pop,nsim=99)
g.test
}