R: Separate genotypes per population

seppop {adegenet} | R Documentation

## 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

### 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)

[Package adegenet version 2.1.4 Index]