genind class | R Documentation |
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 $.
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 of tab
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
names
ploidy
:(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 individual
hierarchy
:(accessor: hier
) (optional,
currently unused) a hierarchical formula
defining the
hierarchical levels in the @@strata
slot.
pop
:(accessor: pop
) (optional) factor
giving the population of each individual
other
:(accessor: other
) (optional) a
list containing other information
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.
Class "gen"
, directly.
Class "indInfo"
, directly.
signature(x = "genind")
: give the names of the
components of a genind object
signature(x = "genind")
: prints a genind object
signature(object = "genind")
: shows a genind
object (same as print)
signature(object = "genind")
: summarizes a
genind object, invisibly returning its content or suppress printing of auxiliary information by specifying verbose = FALSE
Thibaut Jombart t.jombart@imperial.ac.uk
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
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)
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