Construct a family identifier from pedigree information
Usage
# S4 method for class 'character'
make_famid(obj, dadid, momid)
# S4 method for class 'Pedigree'
make_famid(obj)Details
Create a vector of length n, giving the family 'tree' number of each subject. If the Pedigree is totally connected, then everyone will end up in tree 1, otherwise the tree numbers represent the disconnected subfamilies. Singleton subjects give a zero for family number.
Examples
make_famid(
c("A", "B", "C", "D", "E", "F"),
c("C", "D", "0", "0", "0", "0"),
c("E", "E", "0", "0", "0", "0")
)
#> [1] "1" "1" "1" "1" "1" NA
data(sampleped)
ped1 <- Pedigree(sampleped[,-1])
make_famid(ped1)
#> Pedigree object with:
#> Ped object with 55 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
#> ... ... ... ... ... ... ...
#> 2_210 2_210 2_203 2_204 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_213 2_213 2_209 2_208 2 male 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_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
#> ... ... ... ... ... ... ...
#> 2_210 FALSE <NA> FALSE FALSE FALSE FALSE
#> 2_211 FALSE <NA> TRUE FALSE FALSE FALSE
#> 2_212 FALSE <NA> TRUE FALSE FALSE FALSE
#> 2_213 FALSE <NA> FALSE 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_101 FALSE <NA> <NA> FALSE 1968-01-22 <NA>
#> 1_102 TRUE <NA> <NA> FALSE 1975-06-27 <NA>
#> 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>
#> ... ... ... ... ... ... ...
#> 2_210 FALSE <NA> <NA> FALSE <NA> <NA>
#> 2_211 FALSE <NA> <NA> FALSE <NA> <NA>
#> 2_212 FALSE <NA> <NA> FALSE <NA> <NA>
#> 2_213 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_101 <NA> <NA> <NA> 1 1
#> 1_102 <NA> <NA> <NA> 1 1
#> 1_103 <NA> <NA> <NA> 4 4
#> 1_104 <NA> <NA> <NA> 4 4
#> 1_105 <NA> <NA> <NA> 4 4
#> ... ... ... ... ... ...
#> 2_210 <NA> <NA> <NA> 0 0
#> 2_211 <NA> <NA> <NA> 0 0
#> 2_212 <NA> <NA> <NA> 0 0
#> 2_213 <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_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
#> ... ... ... ... ... ...
#> 2_210 0 0 2 <NA> 0
#> 2_211 0 0 1 <NA> 0
#> 2_212 0 0 3 <NA> 0
#> 2_213 0 0 2 <NA> 0
#> 2_214 0 1 0 <NA> 1
#> avail_mods
#> col_class <character>
#> 1_101 0
#> 1_102 0
#> 1_103 0
#> 1_104 0
#> 1_105 0
#> ... ...
#> 2_210 0
#> 2_211 1
#> 2_212 1
#> 2_213 0
#> 2_214 1
#> Rel object with 0 relationshipswith 0 MZ twin, 0 DZ twin, 0 UZ twin, 0 Spouse:
#> id1 id2 code famid
#> <character> <character> <c("ordered", "factor")> <character>