Hints object

The hints are used to specify the order of the individuals in the pedigree and to specify the order of the spouses.

Constructor :

You either need to provide horder or spouse in the dedicated parameters (together or separately), or inside a list.

Usage

Hints(horder, spouse)

# S4 method for class 'list,missing_OR_NULL'
Hints(horder, spouse)

# S4 method for class 'numeric,data.frame'
Hints(horder, spouse)

# S4 method for class 'numeric,missing_OR_NULL'
Hints(horder, spouse)

Arguments

horder: A named numeric vector with one element per subject in the Pedigree. It determines the relative horizontal order of subjects within a sibship, as well as the relative order of processing for the founder couples. (For this latter, the female founders are ordered as though they were sisters). The names of the vector should be the individual identifiers.
spouse: A data.frame with one row per hinted marriage, usually only a few marriages in a pedigree will need an added hint, for instance reverse the plot order of a husband/wife pair. Each row contains the id of the left spouse (i.e. idl), the id of the right hand spouse (i.e. idr), and the anchor (i.e : anchor : 1 = left, 2 = right, 0 = either). Children will preferentially appear under the parents of the anchored spouse.

Value

A Hints object.

Slots

horder: A numeric named vector with one element per subject in the Pedigree. It determines the relative horizontal order of subjects within a sibship, as well as the relative order of processing for the founder couples. (For this latter, the female founders are ordered as though they were sisters).
spouse: A data.frame with one row per hinted marriage, usually only a few marriages in a Pedigree will need an added hint, for instance reverse the plot order of a husband/wife pair. Each row contains the identifiers of the left spouse, the right hand spouse, and the anchor (i.e : 1 = left, 2 = right, 0 = either).

Accessors

horder(x) : Get the horder vector

horder(x) <- value : Set the horder vector

spouse(x) : Get the spouse data.frame

spouse(x) <- value : Set the spouse data.frame

Generics

as.list(x): Convert a Hints object to a list

subset(x, i, keep = TRUE): Subset a Hints object based on the individuals identifiers given.
- i : A vector of individuals identifiers to keep.
- keep : A logical value indicating if the individuals should be kept or deleted.

Examples


Hints(
    list(
        horder = c("1" = 1, "2" = 2, "3" = 3),
        spouse = data.frame(
            idl = c("1", "2"),
            idr = c("2", "3"),
            anchor = c(1, 2)
        )
    )
)
#> An object of class "Hints"
#> Slot "horder":
#> 1 2 3 
#> 1 2 3 
#> 
#> Slot "spouse":
#> [1] idl    idr    anchor
#> <0 rows> (or 0-length row.names)
#> 

Hints(
    horder = c("1" = 1, "2" = 2, "3" = 3),
    spouse = data.frame(
        idl = c("1", "2"),
        idr = c("2", "3"),
        anchor = c(1, 2)
    )
)
#> An object of class "Hints"
#> Slot "horder":
#> 1 2 3 
#> 1 2 3 
#> 
#> Slot "spouse":
#>   idl idr anchor
#> 1   1   2   left
#> 2   2   3  right
#> 

Hints(
    horder = c("1" = 1, "2" = 2, "3" = 3)
)
#> An object of class "Hints"
#> Slot "horder":
#> 1 2 3 
#> 1 2 3 
#> 
#> Slot "spouse":
#> [1] idl    idr    anchor
#> <0 rows> (or 0-length row.names)
#>