genind class {adegenet} | R Documentation |
adegenet formal class (S4) for individual genotypes
Description
The S4 class genind
is used to store individual genotypes.
It contains several components described in the 'slots' section).
The summary
of a genind
object invisibly returns a list of component.
The function .valid.genind
is for internal use.
The function genind
creates a genind object from a valid table
of alleles corresponding to the @tab
slot.
Note that as in other S4 classes, slots are accessed using @ instead
of $.
Slots
tab
:-
(accessor:
tab
) matrix integers containing genotypes data for individuals (in rows) for all alleles (in columns). The table differs depending on the@type
slot:
- 'codom': values are numbers of alleles, summing up to the individuals' ploidies.
- 'PA': values are presence/absence of alleles.
In all cases, rows and columns are given generic names. loc.fac
:(accessor:
locFac
) locus factor for the columns oftab
loc.n.all
:(accessor:
nAll
) integer vector giving the number of observed alleles per locus (see note)all.names
:(accessor:
alleles
) list having one component per locus, each containing a character vector of allele namesploidy
:(accessor:
ploidy
) an integer vector indicating the degree of ploidy of the genotypes. Beware: 2 is not an integer, but 2L or as.integer(2) is.type
:a character string indicating the type of marker: 'codom' stands for 'codominant' (e.g. microstallites, allozymes); 'PA' stands for 'presence/absence' (e.g. AFLP).
call
:the matched call
strata
:(accessor:
strata
) (optional) data frame giving levels of population stratification for each individualhierarchy
:(accessor:
hier
) (optional, currently unused) a hierarchicalformula
defining the hierarchical levels in the@@strata
slot.pop
:(accessor:
pop
) (optional) factor giving the population of each individualother
:(accessor:
other
) (optional) a list containing other information
Note:
The loc.n.all
slot will reflect the number of columns per locus that
contain at least one observation. This means that the sum of the this vector
will not necessarily equal the number of columns in the data unless you use
drop = TRUE
when subsetting.
Extends
Class "gen"
, directly.
Class "indInfo"
, directly.
Methods
- names
signature(x = "genind")
: give the names of the components of a genind objectsignature(x = "genind")
: prints a genind object- show
signature(object = "genind")
: shows a genind object (same as print)- summary
signature(object = "genind")
: summarizes a genind object, invisibly returning its content or suppress printing of auxiliary information by specifyingverbose = FALSE
Author(s)
Thibaut Jombart t.jombart@imperial.ac.uk
See Also
as.genind
, genind2genpop
,
genpop
, import2genind
,
read.genetix
, read.genepop
,
read.fstat
Related classes:
- genpop for storing data per populations
- genlight for an efficient storage of binary SNPs genotypes
Examples
showClass("genind")
obj <- read.genetix(system.file("files/nancycats.gtx",package="adegenet"))
obj
validObject(obj)
summary(obj)
## Not run:
# test inter-colonies structuration
if(require(hierfstat)){
gtest <- gstat.randtest(obj,nsim=99)
gtest
plot(gtest)
}
# perform a between-class PCA
pca1 <- dudi.pca(scaleGen(obj, NA.method="mean"),scannf=FALSE,scale=FALSE)
pcabet1 <- between(pca1,obj@pop,scannf=FALSE)
pcabet1
s.class(pcabet1$ls,obj@pop,sub="Inter-class PCA",possub="topleft",csub=2)
add.scatter.eig(pcabet1$eig,2,xax=1,yax=2)
## End(Not run)