Update the family prefix in the individuals identifiers. Individuals identifiers are constructed as follow famid_id. Therefore to update their family prefix the ids are split by the first underscore and the first part is overwritten by famid.
Usage
# S4 method for class 'character,ANY'
upd_famid(obj, famid, missid = NA_character_)
# S4 method for class 'Ped,character_OR_integer'
upd_famid(obj, famid)
# S4 method for class 'Ped,missing'
upd_famid(obj)
# S4 method for class 'Rel,character_OR_integer'
upd_famid(obj, famid)
# S4 method for class 'Rel,missing'
upd_famid(obj)
# S4 method for class 'Pedigree,character_OR_integer'
upd_famid(obj, famid)
# S4 method for class 'Pedigree,missing'
upd_famid(obj)Arguments
- obj
Ped or Pedigree object or a character vector of individual ids
- famid
A character vector with the family identifiers of the individuals. If provide, will be aggregated to the individuals identifiers separated by an underscore.
- 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_.
Details
If famid is missing, then the famid() function will be called
on the object.
Examples
upd_famid(c("1", "2", "B_3"), c("A", "B", "A"))
#> [1] "A_1" "B_2" "A_3"
upd_famid(c("1", "B_2", "C_3", "4"), c("A", NA, "A", NA))
#> [1] "A_1" "2" "A_3" "4"
data(sampleped)
ped1 <- Pedigree(sampleped[,-1])
id(ped(ped1))
#> [1] "101" "102" "103" "104" "105" "106" "107" "108" "109" "110" "111" "112"
#> [13] "113" "114" "115" "116" "117" "118" "119" "120" "121" "122" "123" "124"
#> [25] "125" "126" "127" "128" "129" "130" "131" "132" "133" "134" "135" "136"
#> [37] "137" "138" "139" "140" "141" "201" "202" "203" "204" "205" "206" "207"
#> [49] "208" "209" "210" "211" "212" "213" "214"
new_fam <- make_famid(id(ped(ped1)), dadid(ped(ped1)), momid(ped(ped1)))
id(ped(upd_famid(ped1, new_fam)))
#> [1] "1_101" "1_102" "1_103" "1_104" "1_105" "1_106" "1_107" "1_108" "1_109"
#> [10] "1_110" "1_111" "1_112" "113" "1_114" "1_115" "1_116" "1_117" "1_118"
#> [19] "1_119" "1_120" "1_121" "1_122" "1_123" "1_124" "1_125" "1_126" "1_127"
#> [28] "1_128" "1_129" "1_130" "1_131" "1_132" "1_133" "1_134" "1_135" "1_136"
#> [37] "1_137" "1_138" "1_139" "1_140" "1_141" "2_201" "2_202" "2_203" "2_204"
#> [46] "2_205" "2_206" "2_207" "2_208" "2_209" "2_210" "2_211" "2_212" "2_213"
#> [55] "2_214"
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>