as-methods: Converting genind/genpop objects to other classes

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

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 [e-mail]

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)

thibautjombart/adegenet documentation built on Feb. 8, 2025, 12:09 a.m.