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 13 metadata columns:
#> id dadid momid sex famid steril
#> col_class <character> <character> <character> <ordered> <character> <logical>
#> 1_101 1_101 <NA> <NA> male 1 <NA>
#> 1_102 1_102 <NA> <NA> female 1 <NA>
#> 1_103 1_103 1_135 1_136 male 1 <NA>
#> 1_104 1_104 <NA> <NA> female 1 <NA>
#> 1_105 1_105 <NA> <NA> male 1 <NA>
#> ... ... ... ... ... ... ...
#> 2_210 2_210 2_203 2_204 male 2 <NA>
#> 2_211 2_211 2_203 2_204 male 2 <NA>
#> 2_212 2_212 2_209 2_208 female 2 <NA>
#> 2_213 2_213 2_209 2_208 male 2 <NA>
#> 2_214 2_214 2_209 2_208 male 2 <NA>
#> status avail affected useful kin isinf
#> col_class <logical> <logical> <logical> <logical> <numeric> <logical>
#> 1_101 <NA> FALSE FALSE <NA> <NA> <NA>
#> 1_102 <NA> FALSE TRUE <NA> <NA> <NA>
#> 1_103 <NA> FALSE TRUE <NA> <NA> <NA>
#> 1_104 <NA> FALSE FALSE <NA> <NA> <NA>
#> 1_105 <NA> FALSE <NA> <NA> <NA> <NA>
#> ... ... ... ... ... ... ...
#> 2_210 <NA> FALSE FALSE <NA> <NA> <NA>
#> 2_211 <NA> TRUE FALSE <NA> <NA> <NA>
#> 2_212 <NA> TRUE FALSE <NA> <NA> <NA>
#> 2_213 <NA> FALSE FALSE <NA> <NA> <NA>
#> 2_214 <NA> TRUE TRUE <NA> <NA> <NA>
#> num_child_tot num_child_dir num_child_ind | indId fatherId
#> col_class <numeric> <numeric> <numeric> <character> <character>
#> 1_101 1 1 0 101 <NA>
#> 1_102 1 1 0 102 <NA>
#> 1_103 4 4 0 103 135
#> 1_104 4 4 0 104 <NA>
#> 1_105 4 4 0 105 <NA>
#> ... ... ... ... ... ...
#> 2_210 0 0 0 210 203
#> 2_211 0 0 0 211 203
#> 2_212 0 0 0 212 209
#> 2_213 0 0 0 213 209
#> 2_214 0 0 0 214 209
#> motherId gender affection available num
#> col_class <character> <character> <character> <character> <character>
#> 1_101 <NA> 1 0 0 2
#> 1_102 <NA> 2 1 0 3
#> 1_103 136 1 1 0 2
#> 1_104 <NA> 2 0 0 4
#> 1_105 <NA> 1 <NA> 0 6
#> ... ... ... ... ... ...
#> 2_210 204 1 0 0 2
#> 2_211 204 1 0 1 1
#> 2_212 208 2 0 1 3
#> 2_213 208 1 0 0 2
#> 2_214 208 1 1 1 0
#> error family sterilisation vitalStatus affection_mods
#> col_class <character> <character> <character> <character> <character>
#> 1_101 <NA> <NA> <NA> <NA> 0
#> 1_102 <NA> <NA> <NA> <NA> 1
#> 1_103 <NA> <NA> <NA> <NA> 1
#> 1_104 <NA> <NA> <NA> <NA> 0
#> 1_105 <NA> <NA> <NA> <NA> NA
#> ... ... ... ... ... ...
#> 2_210 <NA> <NA> <NA> <NA> 0
#> 2_211 <NA> <NA> <NA> <NA> 0
#> 2_212 <NA> <NA> <NA> <NA> 0
#> 2_213 <NA> <NA> <NA> <NA> 0
#> 2_214 <NA> <NA> <NA> <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>