# Accessors for adegenet objects An accessor is a function that allows to interact with slots of an object in a convenient way. Several accessors are available for genind or genpop objects. The operator "$" and "$<-" are used to access the slots, being equivalent to "@" and "@<-". 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. UTF-8 methods ## Methods - **nInd**: returns the number of individuals in the `genind` object - **nLoc**: returns the number of loci - **nAll**: returns the number of observed alleles in each locus - **nPop**: returns the number of populations - **pop**: returns a factor assigning individuals to populations. - **pop<-**: replacement method for the `@pop` slot of an object. - **popNames**: returns the names of populations. - **popNames<-**: sets the names of populations using a vector of length `nPop(x)`. - **indNames**: returns the names of individuals. - **indNames<-**: sets the names of individuals using a vector of length `nInd(x)`. - **locNames**: returns the names of markers and/or alleles. - **locNames<-**: sets the names of markers using a vector of length `nLoc(x)`. - **locFac**: returns a factor that defines which locus each column of the `@tab` slot belongs to - **ploidy**: returns the ploidy of the data. - **ploidy<-**: sets the ploidy of the data using an integer. - **alleles**: returns the alleles of each locus. - **alleles<-**: sets the alleles of each locus using a list with one character vector for each locus. - **other**: returns the content of the `@other` slot (misc. information); returns `NULL` if the slot is onlyObserved or of length zero. - **other<-**: 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. ```r 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, ...) ``` ## Arguments - `x`: a genind or a genpop object. - `onlyObserved`: a logical indicating whether the allele count should also include the alleles with onlyObserved columns in the matrix. Defaults to `FALSE`, which will report only the observed alleles in the given population. `onlyObserved = TRUE` will be the equivalent of `table(locFac(x))`, but faster. - `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). ## Returns A genind or genpop object. ## Author(s) Thibaut Jombart t.jombart@imperial.ac.uk ## Details 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. ## Examples ```r 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 is ```

accessors function