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Ped object

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

S4 class to represent the identity informations of the individuals 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.

The metadata will correspond to the columns that do not correspond to the Ped slots.

Usage

# S4 method for class 'data.frame'
Ped(obj, cols_used_init = FALSE, cols_used_del = FALSE)

# S4 method for class 'character_OR_integer'
Ped(
  obj,
  sex,
  dadid,
  momid,
  famid = NA,
  steril = NA,
  status = NA,
  avail = NA,
  affected = NA,
  missid = NA_character_,
  useful = NA,
  isinf = NA,
  kin = NA_real_
)

Arguments

obj

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

cols_used_init

Boolean defining if the columns that will be used should be initialised to NA.

cols_used_del

Boolean defining if the columns that will be used should be deleted.

sex

A character, factor or numeric vector corresponding to the gender of the individuals. This will be transformed to an ordered factor with the following levels: male < female < unknown < terminated The following values are recognized:

  • character() or factor() : "f", "m", "woman", "man", "male", "female", "unknown", "terminated"

  • numeric() : 1 = "male", 2 = "female", 3 = "unknown", 4 = "terminated"

dadid

A vector containing for each subject, the identifiers of the biologicals fathers.

momid

A vector containing for each subject, the identifiers of the biologicals mothers.

famid

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

steril

A logical vector with the sterilisation status of the individuals (i.e. FALSE = not sterilised, TRUE = sterilised, NA = unknown).

status

A logical vector with the affection status of the individuals (i.e. FALSE = alive, TRUE = dead, NA = unknown).

avail

A logical vector with the availability status of the individuals (i.e. FALSE = not available, TRUE = available, NA = unknown).

affected

A logical vector with the affection status of the individuals (i.e. FALSE = unaffected, TRUE = affected, NA = unknown).

missid

A character vector with the missing values identifiers. All the id, dadid and momid corresponding to those values will be set to NA_character_.

useful

A logical vector with the usefulness status of the individuals (i.e. FALSE = not useful, TRUE = useful).

isinf

A logical vector indicating if the individual is informative or not (i.e. FALSE = not informative, TRUE = informative).

kin

A numeric vector with minimal kinship value between the individuals and the informative individuals.

Value

A Ped object.

Details

The minimal needed informations are id, dadid, momid and sex. The other slots are used to store recognized informations. Additional columns can be added to the Ped object and will be stored in the elementMetadata slot of the Ped object.

Slots

id

A character vector with the id of the individuals.

dadid

A character vector with the id of the father of the individuals.

momid

A character vector with the id of the mother of the individuals.

sex

An ordered factor vector for the sex of the individuals (i.e. male < female < unknown < terminated).

famid

A character vector with the family identifiers of the individuals (optional).

steril

A logical vector with the sterilisation status of the individuals (i.e. FALSE = not sterilised, TRUE = sterilised, NA = unknown).

status

A logical vector with the affection status of the individuals (i.e. FALSE = alive, TRUE = dead, NA = unknown).

avail

A logical vector with the availability status of the individuals (i.e. FALSE = not available, TRUE = available, NA = unknown).

affected

A logical vector with the affection status of the individuals (i.e. FALSE = not affected, TRUE = affected, NA = unknown).

useful

A logical vector with the usefulness status of the individuals (i.e. FALSE = not useful, TRUE = useful).

isinf

A logical vector indicating if the individual is informative or not (i.e. FALSE = not informative, TRUE = informative).

kin

A numeric vector with minimal kinship value between the individuals and the useful individuals.

num_child_tot

A numeric vector with the total number of children of the individuals.

num_child_dir

A numeric vector with the number of children of the individuals.

num_child_ind

A numeric vector with the number of children of the individuals.

elementMetadata

A DataFrame with the additional metadata columns of the Ped object.

metadata

Meta informations about the pedigree.

Accessors

For all the following accessors, the x parameters is a Ped object. Each getters return a vector of the same length as x with the values of the corresponding slot. For each getter, you have a setter with the same name, to be use as slot(x) <- value. The value parameter is a vector of the same length as x, except for the mcols() accessors where value is a list or a data.frame with each elements with the same length as x.

  • id(x) : Individuals identifiers

  • dadid(x) : Individuals' father identifiers

  • momid(x) : Individuals' mother identifiers

  • famid(x) : Individuals' family identifiers

  • sex(x) : Individuals' gender

  • affected(x) : Individuals' affection status

  • avail(x) : Individuals' availability status

  • status(x) : Individuals' death status

  • isinf(x) : Individuals' informativeness status

  • kin(x) : Individuals' kinship distance to the informative individuals

  • useful(x) : Individuals' usefullness status

  • mcols(x) : Individuals' metadata

Generics

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

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

  • as.list(x): Convert a Ped object to a list with the metadata columns at the end.

  • as.data.frame(x): Convert a Ped object to a data.frame with the metadata columns at the end.

  • subset(x, i, del_parents = FALSE, keep = TRUE): Subset a Ped object based on the individuals identifiers given.

    • i : A vector of individuals identifiers to keep.

    • del_parents : A value indicating if the parents of the individuals should be deleted.

    • keep : A logical value indicating if the individuals should be kept or deleted.

See also

Pedigree()

Examples


data(sampleped)
Ped(sampleped)
#> Ped object with 55 individuals and 2 metadata columns:
#>                    id       dadid       momid       sex       famid    steril
#> col_class <character> <character> <character> <ordered> <character> <logical>
#> 101               101        <NA>        <NA>      male           1      <NA>
#> 102               102        <NA>        <NA>    female           1      <NA>
#> 103               103         135         136      male           1      <NA>
#> 104               104        <NA>        <NA>    female           1      <NA>
#> 105               105        <NA>        <NA>      male           1      <NA>
#> ...               ...         ...         ...       ...         ...       ...
#> 210               210         203         204      male           2      <NA>
#> 211               211         203         204      male           2      <NA>
#> 212               212         209         208    female           2      <NA>
#> 213               213         209         208      male           2      <NA>
#> 214               214         209         208      male           2      <NA>
#>              status     avail  affected    useful       kin     isinf
#> col_class <logical> <logical> <logical> <logical> <numeric> <logical>
#> 101            <NA>     FALSE      <NA>      <NA>      <NA>      <NA>
#> 102            <NA>     FALSE      <NA>      <NA>      <NA>      <NA>
#> 103            <NA>     FALSE      <NA>      <NA>      <NA>      <NA>
#> 104            <NA>     FALSE      <NA>      <NA>      <NA>      <NA>
#> 105            <NA>     FALSE      <NA>      <NA>      <NA>      <NA>
#> ...             ...       ...       ...       ...       ...       ...
#> 210            <NA>     FALSE      <NA>      <NA>      <NA>      <NA>
#> 211            <NA>      TRUE      <NA>      <NA>      <NA>      <NA>
#> 212            <NA>      TRUE      <NA>      <NA>      <NA>      <NA>
#> 213            <NA>     FALSE      <NA>      <NA>      <NA>      <NA>
#> 214            <NA>      TRUE      <NA>      <NA>      <NA>      <NA>
#>           num_child_tot num_child_dir num_child_ind |   affection         num
#> col_class     <numeric>     <numeric>     <numeric>   <character> <character>
#> 101                   1             1             0             0           2
#> 102                   1             1             0             1           3
#> 103                   4             4             0             1           2
#> 104                   4             4             0             0           4
#> 105                   4             4             0          <NA>           6
#> ...                 ...           ...           ...           ...         ...
#> 210                   0             0             0             0           2
#> 211                   0             0             0             0           1
#> 212                   0             0             0             0           3
#> 213                   0             0             0             0           2
#> 214                   0             0             0             1           0

Ped(
    obj = c("1", "2", "3", "4", "5", "6"),
    dadid = c("4", "4", "6", "0", "0", "0"),
    momid = c("5", "5", "5", "0", "0", "0"),
    sex = c(1, 2, 3, 1, 2, 1),
    missid = "0"
)
#> Ped object with 6 individuals and 0 metadata columns:
#>                    id       dadid       momid       sex       famid    steril
#> col_class <character> <character> <character> <ordered> <character> <logical>
#> 1                   1           4           5      male        <NA>      <NA>
#> 2                   2           4           5    female        <NA>      <NA>
#> 3                   3           6           5   unknown        <NA>      <NA>
#> 4                   4        <NA>        <NA>      male        <NA>      <NA>
#> 5                   5        <NA>        <NA>    female        <NA>      <NA>
#> 6                   6        <NA>        <NA>      male        <NA>      <NA>
#>              status     avail  affected    useful       kin     isinf
#> col_class <logical> <logical> <logical> <logical> <numeric> <logical>
#> 1              <NA>      <NA>      <NA>      <NA>      <NA>      <NA>
#> 2              <NA>      <NA>      <NA>      <NA>      <NA>      <NA>
#> 3              <NA>      <NA>      <NA>      <NA>      <NA>      <NA>
#> 4              <NA>      <NA>      <NA>      <NA>      <NA>      <NA>
#> 5              <NA>      <NA>      <NA>      <NA>      <NA>      <NA>
#> 6              <NA>      <NA>      <NA>      <NA>      <NA>      <NA>
#>           num_child_tot num_child_dir num_child_ind
#> col_class     <numeric>     <numeric>     <numeric>
#> 1                     0             0             0
#> 2                     0             0             0
#> 3                     0             0             0
#> 4                     3             2             1
#> 5                     3             3             0
#> 6                     3             1             2