adegenet: isPoly – R documentation

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isPoly

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)

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release