R: Assess polymorphism in genind/genpop objects

isPoly-methods {adegenet} | R Documentation

## Assess polymorphism in genind/genpop objects

### Description

The simple function `isPoly` can be used to check which loci are polymorphic, or alternatively to check which alleles give rise to polymorphism.

### Usage

    ## S4 method for signature 'genind'
    isPoly(x, by=c("locus","allele"), thres=1/100)
    ## S4 method for signature 'genpop'
    isPoly(x, by=c("locus","allele"), thres=1/100)

### Arguments

`x` | a genind and genpop object
`by` | a character being "locus" or "allele", indicating whether results should indicate polymorphic loci ("locus"), or alleles giving rise to polymorphism ("allele").
`thres` | a numeric value giving the minimum frequency of an allele giving rise to polymorphism (defaults to 0.01).

### Value

A vector of logicals.

### Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

### Examples

    ## Not run:
    data(nancycats)
    isPoly(nancycats,by="loc", thres=0.1)
    isPoly(nancycats[1:3],by="loc", thres=0.1)
    genind2df(nancycats[1:3])

    ## End(Not run)

[Package adegenet version 2.1.4 Index]