Accessors for adegenet objects
The operator "[" is a flexible way to subset data by individuals,
populations, alleles, and loci. When using a matrix-like syntax,
subsetting will apply to the dimensios of the @tab slot. In addition,
specific arguments loc and pop can be used to indicate
subsets of loci and populations. The argument drop is a logical
indicating if alleles becoming non-polymorphic in a new dataset should
be removed (default: FALSE). Examples:
"obj[i,j]" returns "obj" with a subset 'i' of individuals and 'j' of
alleles.
"obj[1:10,]" returns an object with only the first 10 genotypes (if
"obj" is a genind) or the first 10 populations (if
"obj" is a genpop)
"obj[1:10, 5:10]" returns an object keeping the first 10 entities and
the alleles 5 to 10.
"obj[loc=c(1,3)]" returns an object keeping only the 1st and 3rd
loci, using locNames(obj) as reference; logicals, or named loci
also work; this overrides other subsetting of alleles.
"obj[pop=2:4]" returns an object keeping only individuals from the
populations 2, 3 and 4, using popNames(obj) as reference;
logicals, or named populations also work; this overrides other
subsetting of individuals.
"obj[i=1:2, drop=TRUE]" returns an object keeping only the first
two individuals (or populations), dropping the alleles no longer
present in the data.
The argument treatOther handles the treatment of objects in the
@other slot (see details). The argument drop can be set
to TRUE to drop alleles that are no longer represented in the subset.
nInd(x, ...) nLoc(x, ...) nAll(x, onlyObserved = FALSE, ...) nPop(x, ...) pop(x) indNames(x, ...) ## S4 method for signature 'genind' indNames(x, ...) locNames(x, ...) ## S4 method for signature 'genind' locNames(x, withAlleles=FALSE, ...) ## S4 method for signature 'genpop' locNames(x, withAlleles=FALSE, ...) popNames(x, ...) ## S4 method for signature 'genind' popNames(x, ...) popNames(x, ...) ## S4 method for signature 'genpop' popNames(x, ...) ploidy(x, ...) ## S4 method for signature 'genind' ploidy(x, ...) ## S4 method for signature 'genpop' ploidy(x, ...) ## S4 method for signature 'genind' other(x, ...) ## S4 method for signature 'genpop' other(x, ...)
x |
|
onlyObserved |
a logical indicating whether the allele count should
also include the alleles with onlyObserved columns in the matrix. Defaults
to |
withAlleles |
a logical indicating whether the result should be of the form [locus name].[allele name], instead of [locus name]. |
... |
further arguments to be passed to other methods (currently not used). |
The "[" operator can treat elements in the @other slot as
well. For instance, if obj@other$xy contains spatial
coordinates, the obj[1:3, ]@other$xy will contain the spatial
coordinates of the genotypes (or population) 1,2 and 3. This is
handled through the argument treatOther, a logical defaulting
to TRUE. If set to FALSE, the @other returned unmodified.
Note that only matrix-like, vector-like and lists can be proceeded in
@other. Other kind of objects will issue a warning an be
returned as they are, unless the argument quiet is left to
TRUE, its default value.
The drop argument can be set to TRUE to retain only alleles
that are present in the subset. To achieve better control of
polymorphism of the data, see isPoly.
nAll() reflects the number of columns per locus present in the current
gen object. If onlyObserved = TRUE, then the number of columns with at
least one non-missing allele is shown.
returns the number of individuals in the genind object
returns the number of loci
returns the number of observed alleles in each locus
returns the number of populations
returns a factor assigning individuals to populations.
replacement method for the @pop slot of an
object.
returns the names of populations.
sets the names of populations using a vector of
length nPop(x).
returns the names of individuals.
sets the names of individuals using a vector of
length nInd(x).
returns the names of markers and/or alleles.
sets the names of markers using a vector of
length nLoc(x).
returns a factor that defines which locus each column of the @tab slot belongs to
returns the ploidy of the data.
sets the ploidy of the data using an integer.
returns the alleles of each locus.
sets the alleles of each locus using a list with one character vector for each locus.
returns the content of the @other slot
(misc. information); returns NULL if the slot is onlyObserved or of
length zero.
sets the content of the @other slot
(misc. information); the provided value needs to be a list; it
not, provided value will be stored within a list.
Thibaut Jombart t.jombart@imperial.ac.uk
data(nancycats)
nancycats
pop(nancycats) # get the populations
indNames(nancycats) # get the labels of individuals
locNames(nancycats) # get the labels of the loci
alleles(nancycats) # get the alleles
nAll(nancycats) # count the number of alleles
head(tab(nancycats)) # get allele counts
# get allele frequencies, replace NAs
head(tab(nancycats, freq = TRUE, NA.method = "mean"))
# let's isolate populations 4 and 8
popNames(nancycats)
obj <- nancycats[pop=c(4, 8)]
obj
popNames(obj)
pop(obj)
nAll(obj, onlyObserved = TRUE) # count number of alleles among these two populations
nAll(obj) # count number of columns in the data
all(nAll(obj, onlyObserved = TRUE) == lengths(alleles(obj))) # will be FALSE since drop = FALSE
all(nAll(obj) == lengths(alleles(obj))) # will be FALSE since drop = FALSE
# let's isolate two markers, fca23 and fca90
locNames(nancycats)
obj <- nancycats[loc=c("fca23","fca90")]
obj
locNames(obj)
# illustrate pop
obj <- nancycats[sample(1:100, 10)]
pop(obj)
pop(obj) <- rep(c('b', 'a'), each = 5)
pop(obj)
# illustrate locNames
locNames(obj)
locNames(obj, withAlleles = TRUE)
locNames(obj)[1] <- "newLocus"
locNames(obj)
locNames(obj, withAlleles=TRUE)
# illustrate how 'other' slot is handled
data(sim2pop)
nInd(sim2pop)
other(sim2pop[1:6]) # xy is subsetted automatically
other(sim2pop[1:6, treatOther=FALSE]) # xy is left as isPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.