R: Converting genind/genpop objects to other classes
as methods in adegenet
R Documentation
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".
## 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)