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Rel object

Source: R/AllClass.R, R/AllConstructor.R, R/AllAccessors.R, and 1 more
Rel-class.Rd

S4 class to represent the special relationships in a Pedigree.

Constructor :

You either need to provide a vector of the same size for each slot or a data.frame with the corresponding columns.

Usage

# S4 method for class 'data.frame'
Rel(obj)

# S4 method for class 'character_OR_integer'
Rel(obj, id2, code, famid = NA_character_, group = NA_character_)

Arguments

obj

A character vector with the id of the first individuals of each pairs or a data.frame with all the informations in corresponding columns.

id2

A character vector with the id of the second individuals of each pairs

code

A character, factor or numeric vector corresponding to the relation code of the individuals:

  • MZ twin = Monozygotic twin

  • DZ twin = Dizygotic twin

  • UZ twin = twin of unknown zygosity

  • Spouse = Spouse The following values are recognized:

  • character() or factor() : "MZ twin", "DZ twin", "UZ twin", "Spouse" with of without space between the words. The case is not important.

  • numeric() : 1 = "MZ twin", 2 = "DZ twin", 3 = "UZ twin", 4 = "Spouse"

famid

A character vector with the family identifiers of the individuals. If provide, will be aggregated to the individuals identifiers separated by an underscore.

group

A numeric vector with the set number for twins.

Value

A Rel object.

Details

A Rel object is a list of special relationships between individuals in the pedigree. It is used to create a Pedigree object. The minimal needed informations are id1, id2 and code.

If a famid is provided, the individuals id will be aggregated to the famid character to ensure the uniqueness of the id.

Slots

id1

A character vector with the id of the first individual.

id2

A character vector with the id of the second individual.

code

An ordered factor vector with the code of the special relationship.

(i.e. MZ twin < DZ twin < UZ twin < Spouse).

famid

A character vector with the famid of the individuals.

group

A numeric vector with the set number for twins.

Accessors

For all the following accessors, the x parameters is a Rel object. Each getters return a vector of the same length as x with the values of the corresponding slot.

  • code(x) : Relationships' code

  • id1(x) : Relationships' first individuals' identifier

  • id2(x) : Relationships' second individuals' identifier

  • famid(x) : Relationships' individuals' family identifier

  • famid(x) <- value : Set the relationships' individuals' family identifier

    • value : A character or integer vector of the same length as x with the family identifiers

Generics

  • summary(x): Compute the summary of a Rel object

  • show(x): Convert the Rel object to a data.frame and print it with its summary.

  • as.list(x): Convert a Rel object to a list

  • as.data.frame(x): Convert a Rel object to a data.frame

  • subset(x, i, keep = TRUE): Subset a Rel 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.

See also

Pedigree()

Examples


rel_df <- data.frame(
    id1 = c("1", "2", "3"),
    id2 = c("2", "3", "4"),
    code = c(1, 1, 4)
)
Rel(rel_df)
#> Rel object with 4 relationshipswith 3 MZ twin, 0 DZ twin, 0 UZ twin, 1 Spouse:
#>           id1         id2                     code       famid     group
#>   <character> <character> <c("ordered", "factor")> <character> <numeric>
#> 1           1           2                  MZ twin        <NA>         1
#> 2           1           3                  MZ twin        <NA>         1
#> 3           2           3                  MZ twin        <NA>         1
#> 4           3           4                   Spouse        <NA>      <NA>

Rel(
    obj = c("1", "2", "3"),
    id2 = c("2", "3", "4"),
    code = c(1, 1, 4)
)
#> Rel object with 4 relationshipswith 3 MZ twin, 0 DZ twin, 0 UZ twin, 1 Spouse:
#>           id1         id2                     code       famid     group
#>   <character> <character> <c("ordered", "factor")> <character> <numeric>
#> 1           1           2                  MZ twin        <NA>         1
#> 2           1           3                  MZ twin        <NA>         1
#> 3           2           3                  MZ twin        <NA>         1
#> 4           3           4                   Spouse        <NA>      <NA>