Compute the usefulness of individuals
Usage
# S4 method for class 'character'
useful_inds(
obj,
dadid,
momid,
avail,
affected,
num_child_tot,
id_inf,
keep_infos = FALSE
)
# S4 method for class 'Pedigree'
useful_inds(obj, keep_infos = FALSE, reset = FALSE, max_dist = NULL)
# S4 method for class 'Ped'
useful_inds(obj, keep_infos = FALSE, reset = FALSE, max_dist = NULL)Arguments
- obj
A character vector with the id of the individuals or a
data.framewith all the informations in corresponding columns.- 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.
- 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).- num_child_tot
A numeric vector of the number of children of each individuals
- id_inf
An identifiers vector of informative individuals.
- keep_infos
Boolean to indicate if parents with unknown status but available or reverse should be kept
- reset
Boolean to indicate if the
usefulcolumn should be reset- max_dist
The maximum distance to informative individuals
Details
Check for the informativeness of the individuals based on the
informative parameter given, the number of children and the usefulness
of their parents. A useful slot is added to the Ped object with the
usefulness of the individual.
Examples
data(sampleped)
ped1 <- Pedigree(sampleped[sampleped$famid == "1",])
ped1 <- is_informative(ped1, informative = "AvAf", col_aff = "affection")
ped(useful_inds(ped1))
#> Ped object with 41 individuals and 5 metadata columns:
#> id dadid momid famid sex fertility
#> col_class <character> <character> <character> <character> <ordered> <factor>
#> 1_101 1_101 <NA> <NA> 1 male fertile
#> 1_102 1_102 <NA> <NA> 1 female fertile
#> 1_103 1_103 1_135 1_136 1 male fertile
#> 1_104 1_104 <NA> <NA> 1 female fertile
#> 1_105 1_105 <NA> <NA> 1 male fertile
#> ... ... ... ... ... ... ...
#> 1_137 1_137 <NA> <NA> 1 male fertile
#> 1_138 1_138 1_135 1_136 1 female fertile
#> 1_139 1_139 1_137 1_138 1 male fertile
#> 1_140 1_140 1_137 1_138 1 female fertile
#> 1_141 1_141 1_137 1_138 1 female fertile
#> miscarriage deceased avail evaluated consultand proband
#> col_class <factor> <logical> <logical> <logical> <logical> <logical>
#> 1_101 FALSE <NA> FALSE TRUE FALSE FALSE
#> 1_102 FALSE <NA> FALSE FALSE FALSE FALSE
#> 1_103 FALSE <NA> FALSE FALSE FALSE FALSE
#> 1_104 FALSE <NA> FALSE FALSE FALSE FALSE
#> 1_105 FALSE <NA> FALSE FALSE FALSE FALSE
#> ... ... ... ... ... ... ...
#> 1_137 FALSE <NA> FALSE FALSE FALSE FALSE
#> 1_138 FALSE <NA> FALSE FALSE FALSE FALSE
#> 1_139 FALSE <NA> FALSE FALSE FALSE FALSE
#> 1_140 FALSE <NA> TRUE FALSE FALSE FALSE
#> 1_141 FALSE <NA> TRUE FALSE FALSE FALSE
#> affected carrier asymptomatic adopted dateofbirth dateofdeath
#> col_class <logical> <logical> <logical> <logical> <character> <character>
#> 1_101 <NA> <NA> <NA> FALSE 1968-01-22 <NA>
#> 1_102 <NA> <NA> <NA> FALSE 1975-06-27 <NA>
#> 1_103 <NA> <NA> <NA> FALSE 1975-08-14 <NA>
#> 1_104 <NA> <NA> <NA> FALSE <NA> <NA>
#> 1_105 <NA> <NA> <NA> FALSE <NA> <NA>
#> ... ... ... ... ... ... ...
#> 1_137 <NA> <NA> <NA> FALSE <NA> <NA>
#> 1_138 <NA> <NA> <NA> FALSE <NA> <NA>
#> 1_139 <NA> <NA> <NA> FALSE <NA> <NA>
#> 1_140 <NA> TRUE <NA> FALSE <NA> <NA>
#> 1_141 <NA> <NA> TRUE FALSE <NA> <NA>
#> useful kin isinf num_child_tot num_child_dir
#> col_class <logical> <numeric> <logical> <numeric> <numeric>
#> 1_101 TRUE 3 FALSE 1 1
#> 1_102 TRUE 3 FALSE 1 1
#> 1_103 TRUE 2 FALSE 4 4
#> 1_104 TRUE 2 FALSE 4 4
#> 1_105 TRUE 2 FALSE 4 4
#> ... ... ... ... ... ...
#> 1_137 TRUE Inf FALSE 3 3
#> 1_138 TRUE 3 FALSE 3 3
#> 1_139 TRUE 4 FALSE 0 0
#> 1_140 TRUE 4 FALSE 0 0
#> 1_141 TRUE 4 FALSE 0 0
#> num_child_ind | affection num error affection_mods
#> col_class <numeric> <character> <character> <character> <character>
#> 1_101 0 0 2 <NA> 0
#> 1_102 0 1 3 <NA> 1
#> 1_103 0 1 2 <NA> 1
#> 1_104 0 0 4 <NA> 0
#> 1_105 0 <NA> 6 <NA> NA
#> ... ... ... ... ... ...
#> 1_137 0 <NA> 3 <NA> NA
#> 1_138 0 <NA> 2 <NA> NA
#> 1_139 0 1 3 <NA> 1
#> 1_140 0 0 1 <NA> 0
#> 1_141 0 0 0 <NA> 0
#> avail_mods
#> col_class <character>
#> 1_101 0
#> 1_102 0
#> 1_103 0
#> 1_104 0
#> 1_105 0
#> ... ...
#> 1_137 0
#> 1_138 0
#> 1_139 0
#> 1_140 1
#> 1_141 1