adegenet: as-methods – R documentation

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as-methods

Converting genind/genpop objects to other classes

Description

These S3 and S4 methods are used to coerce genind and genpop objects to matrix-like objects. In most cases, this is equivalent to calling the @tab slot. An exception to this is the convertion to ktab objects used in the ade4 package as inputs for K-tables methods (e.g. Multiple Coinertia Analysis).

Usage

as(object, Class)

Arguments

object: a genind or a genpop object.
Class: the name of the class to which the object should be coerced, for instance "data.frame" or "matrix".

Methods

coerce: from one object class to another using as(object,"Class"), where the object is of the old class and the returned object is of the new class "Class".

Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

Examples

## Not run: 
data(microbov)
x <- tab(microbov,NA.method="mean")
as(x[1:3],"data.frame")

## dudi functions attempt to convert their first argument
## to a data.frame; so they can be used on genind/genpop objects.
## perform a PCA
pca1 <- dudi.pca(x, scale=FALSE, scannf=FALSE)
pca1

x <- genind2genpop(microbov,miss="chi2")
x <- as(x,"ktab")
class(x)
## perform a STATIS analysis
statis1 <- statis(x, scannf=FALSE)
statis1
plot(statis1)


## 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