Find single affected and available individual from a Pedigree
Source:R/find_avail_affected.R
find_avail_affected.RdFinds one subject from among available non-parents with indicated affection status.
Usage
# S4 method for class 'Ped'
find_avail_affected(obj, avail = NULL, affected = NULL, affstatus = NA)
# S4 method for class 'Pedigree'
find_avail_affected(obj, avail = NULL, affected = NULL, affstatus = NA)Arguments
- obj
A Ped or Pedigree object.
- 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).- affstatus
Affection status to search for.
Value
A list is returned with the following components
ped The new Ped object
newAvail Vector of availability status of trimmed individuals
idTrimmed Vector of IDs of trimmed individuals
isTrimmed logical value indicating whether Ped object has been trimmed
bit_size Bit size of the trimmed Ped
Details
When used within shrink(), this function is called
with the first affected indicator,
if the affected item in the Pedigree is a matrix of
multiple affected indicators.
If avail or affected is null, then the function will use the corresponding Ped accessor.
Examples
data(sampleped)
pedi <- Pedigree(sampleped)
find_avail_affected(pedi, affstatus = 1)
#> $ped
#> Ped object with 38 individuals and 5 metadata columns:
#> id dadid momid famid sex fertility
#> col_class <character> <character> <character> <character> <ordered> <factor>
#> 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_106 1_106 <NA> <NA> 1 female fertile
#> 1_109 1_109 <NA> <NA> 1 female fertile
#> ... ... ... ... ... ... ...
#> 2_208 2_208 2_201 2_202 2 female fertile
#> 2_209 2_209 <NA> <NA> 2 male fertile
#> 2_211 2_211 2_203 2_204 2 male fertile
#> 2_212 2_212 2_209 2_208 2 female fertile
#> 2_214 2_214 2_209 2_208 2 male fertile
#> miscarriage deceased avail evaluated consultand proband
#> col_class <factor> <logical> <logical> <logical> <logical> <logical>
#> 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_106 FALSE <NA> FALSE FALSE FALSE FALSE
#> 1_109 FALSE <NA> TRUE FALSE TRUE FALSE
#> ... ... ... ... ... ... ...
#> 2_208 FALSE <NA> FALSE FALSE FALSE FALSE
#> 2_209 FALSE <NA> FALSE FALSE FALSE FALSE
#> 2_211 FALSE <NA> TRUE FALSE FALSE FALSE
#> 2_212 FALSE <NA> TRUE FALSE FALSE FALSE
#> 2_214 FALSE <NA> TRUE FALSE FALSE FALSE
#> affected carrier asymptomatic adopted dateofbirth dateofdeath
#> col_class <logical> <logical> <logical> <logical> <character> <character>
#> 1_103 TRUE <NA> <NA> FALSE 1975-08-14 <NA>
#> 1_104 FALSE <NA> <NA> FALSE <NA> <NA>
#> 1_105 <NA> <NA> <NA> FALSE <NA> <NA>
#> 1_106 <NA> <NA> <NA> FALSE <NA> <NA>
#> 1_109 FALSE <NA> TRUE FALSE <NA> <NA>
#> ... ... ... ... ... ... ...
#> 2_208 FALSE <NA> <NA> FALSE <NA> <NA>
#> 2_209 FALSE <NA> <NA> FALSE <NA> <NA>
#> 2_211 FALSE <NA> <NA> FALSE <NA> <NA>
#> 2_212 FALSE <NA> <NA> FALSE <NA> <NA>
#> 2_214 TRUE <NA> <NA> FALSE <NA> <NA>
#> useful kin isinf num_child_tot num_child_dir
#> col_class <logical> <numeric> <logical> <numeric> <numeric>
#> 1_103 <NA> <NA> <NA> 3 3
#> 1_104 <NA> <NA> <NA> 3 3
#> 1_105 <NA> <NA> <NA> 4 4
#> 1_106 <NA> <NA> <NA> 4 4
#> 1_109 <NA> <NA> <NA> 0 0
#> ... ... ... ... ... ...
#> 2_208 <NA> <NA> <NA> 2 2
#> 2_209 <NA> <NA> <NA> 2 2
#> 2_211 <NA> <NA> <NA> 0 0
#> 2_212 <NA> <NA> <NA> 0 0
#> 2_214 <NA> <NA> <NA> 0 0
#> num_child_ind | affection num error affection_mods
#> col_class <numeric> <character> <character> <character> <character>
#> 1_103 0 1 2 <NA> 1
#> 1_104 0 0 4 <NA> 0
#> 1_105 0 <NA> 6 <NA> NA
#> 1_106 0 <NA> 1 <NA> NA
#> 1_109 0 0 3 <NA> 0
#> ... ... ... ... ... ...
#> 2_208 0 0 1 <NA> 0
#> 2_209 0 0 2 <NA> 0
#> 2_211 0 0 1 <NA> 0
#> 2_212 0 0 3 <NA> 0
#> 2_214 0 1 0 <NA> 1
#> avail_mods
#> col_class <character>
#> 1_103 0
#> 1_104 0
#> 1_105 0
#> 1_106 0
#> 1_109 1
#> ... ...
#> 2_208 0
#> 2_209 0
#> 2_211 1
#> 2_212 1
#> 2_214 1
#>
#> $new_avail
#> [1] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE TRUE FALSE TRUE
#> [13] TRUE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE
#> [25] FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE
#> [37] TRUE TRUE
#>
#> $id_trimmed
#> [1] "1_124"
#>
#> $is_trimmed
#> [1] TRUE
#>
#> $bit_size
#> [1] 37
#>