isPoly: Assess polymorphism in genind/genpop objects

In skayondo/adegenet: Exploratory Analysis of Genetic and Genomic Data

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)

skayondo/adegenet documentation built on July 18, 2020, 12:38 a.m.