R: genind constructor

initialize,genind-method {adegenet} | R Documentation

## genind constructor

### Description

The function `new` has a method for building genind objects. See the class description of genind for more information on this data structure. The functions `genind` and `as.genind` are aliases for `new("genind", ...)`.

### Usage

    ## S4 method for signature 'genind'
    initialize(
      .Object,
      tab,
      pop = NULL,
      prevcall = NULL,
      ploidy = 2L,
      type = c("codom", "PA"),
      strata = NULL,
      hierarchy = NULL,
      ...
    )

    genind(...)

    as.genind(...)

### Arguments

`.Object` | prototyped object (generated automatically when calling 'new')
`tab` | A matrix of integers corresponding to the @tab slot of a genind object, with individuals in rows and alleles in columns, and containing either allele counts (if type="codom") or allele presence/absence (if type="PA")
`pop` | an optional factor with one value per row in `tab` indicating the population of each individual
`prevcall` | an optional call to be stored in the object
`ploidy` | an integer vector indicating the ploidy of the individual; each individual can have a different value; if only one value is provided, it is recycled to generate a vector of the right length.
`type` | a character string indicating the type of marker: codominant ("codom") or presence/absence ("PA")
`strata` | a data frame containing population hierarchies or stratifications in columns. This must be the same length as the number of individuals in the data set.
`hierarchy` | a hierarchical formula defining the columns of the strata slot that are hierarchical. Defaults to NULL.
`...` | further arguments passed to other methods (currently not used)

### Details

Most users do not need using the constructor, but merely to convert raw allele data using `df2genind` and related functions.

### Value

a genind object

### See Also

the description of the genind class; `df2genind`

[Package adegenet version 2.1.4 Index]