adegenet (version 1.4-2)

isPoly-methods: 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

## S3 method for class 'genind':
isPoly(x, by=c("locus","allele"), thres=1/100)
## S3 method for class '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.

Examples

data(nancycats)
isPoly(nancycats,by="loc", thres=0.1)
isPoly(nancycats[1:3],by="loc", thres=0.1)
genind2df(nancycats[1:3])