genind constructor
## 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(...).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 |
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) |
Most users do not need using the constructor, but merely to convert raw allele data using df2genind and related functions.
a genind object
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