seppop: Separate genotypes per population

Description

The function seppop splits a genind or a genlight object by population, returning a list of objects whose components each correspond to a population.

For genind objects, the output can either be a list of genind (default), or a list of matrices corresponding to the @tab slot.

Usage

# S4 method for genind
seppop(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"),
  drop=FALSE, treatOther=TRUE, keepNA = FALSE, quiet=TRUE)
# S4 method for genlight
seppop(x,pop=NULL, treatOther=TRUE, keepNA = FALSE, quiet=TRUE, ...)

Value

According to 'res.type': a list of genind object (default) or a matrix of data corresponding to the 'tab' slots.

Arguments

x: a genind object
pop: a factor giving the population of each genotype in 'x' OR a formula specifying which strata are to be used when converting to a genpop object. If none provided, population factors are sought in x@pop, but if given, the argument prevails on x@pop.
truenames: a logical indicating whether true names should be used (TRUE, default) instead of generic labels (FALSE); used if res.type is "matrix".
res.type: a character indicating the type of returned results, a list of genind object (default) or a matrix of data corresponding to the 'tab' slots.
drop: a logical stating whether alleles that are no longer present in a subset of data should be discarded (TRUE) or kept anyway (FALSE, default).
treatOther: a logical stating whether elements of the @other slot should be treated as well (TRUE), or not (FALSE). See details in accessor documentations (pop).
keepNA: If there are individuals with missing population information, should they be pooled into a separate population (TRUE), or excluded (FALSE, default).
quiet: a logical indicating whether warnings should be issued when trying to subset components of the @other slot (TRUE), or not (FALSE, default).
...: further arguments passed to the genlight constructor.

Author

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

Run this code

if (FALSE) {
data(microbov)
strata(microbov) <- data.frame(other(microbov))

obj <- seppop(microbov)
names(obj)

obj$Salers

### example using strata
obj2 <- seppop(microbov, ~coun/spe)
names(obj2)

obj2$AF_BI

#### example for genlight objects ####
x <- new("genlight", list(a=rep(1,1e3),b=rep(0,1e3),c=rep(1, 1e3)))
x

pop(x) # no population info
pop(x) <- c("pop1","pop2", "pop1") # set population memberships
pop(x)
seppop(x)
as.matrix(seppop(x)$pop1)[,1:20]
as.matrix(seppop(x)$pop2)[,1:20,drop=FALSE]
}