seppop: Separate genotypes per population

In adegenet: Exploratory Analysis of Genetic and Genomic Data

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 signature 'genind'
seppop(x,pop=NULL,truenames=TRUE,res.type=c("genind","matrix"),
  drop=FALSE, treatOther=TRUE, keepNA = FALSE, quiet=TRUE)

## S4 method for signature 'genlight'
seppop(x,pop=NULL, treatOther=TRUE, keepNA = FALSE, quiet=TRUE, ...)

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.

Value

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

Author(s)

Thibaut Jombart [e-mail]

See Also

seploc, repool

Examples

## Not run: 
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]

## End(Not run)

adegenet documentation built on Feb. 16, 2023, 6 p.m.