isPoly: Assess polymorphism in genind/genpop objects

In adegenet: Exploratory Analysis of Genetic and Genomic Data

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 [e-mail]

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)

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