adegenet: seppop – R documentation

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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 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 t.jombart@imperial.ac.uk

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

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release