Shrink Pedigree object to specified bit size with priority placed on trimming uninformative subjects. The algorithm is useful for getting a Pedigree condensed to a minimally informative size for algorithms or testing that are limited by size of the Pedigree.
If avail or affected are NULL, they are extracted
with their corresponding accessors from the Ped object.
Usage
# S4 method for class 'Pedigree'
shrink(obj, avail = NULL, affected = NULL, max_bits = 16)
# S4 method for class 'Ped'
shrink(obj, avail = NULL, affected = NULL, max_bits = 16)Arguments
- obj
A Pedigree or Ped 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).- max_bits
Optional, the bit size for which to shrink the Pedigree
Value
A list containing the following elements:
pedObj: Pedigree object after trimming
id_trim: Vector of ids trimmed from Pedigree
id_lst: List of ids trimmed by category
bit_size: Vector of bit sizes after each trimming step
avail: Vector of availability status after trimming
pedSizeOriginal: Number of subjects in original Pedigree
pedSizeIntermed: Number of subjects after initial trimming
pedSizeFinal: Number of subjects after final trimming
Details
Iteratively remove subjects from the Pedigree. The random removal of members was previously controlled by a seed argument, but we remove this, forcing users to control randomness outside the function. First remove uninformative subjects, i.e., unavailable (not genotyped) with no available descendants. Next, available terminal subjects with unknown phenotype if both parents available. Last, iteratively shrinks Pedigrees by preferentially removing individuals (chosen at random if there are multiple of the same status):
Subjects with unknown affected status
Subjects with unaffected affected status
Affected subjects.
Examples
data(sampleped)
ped1 <- Pedigree(sampleped[sampleped$famid == '1',])
shrink(ped1, max_bits = 12)
#> $pedObj
#> Pedigree object with:
#> Ped object with 13 individuals and 13 metadata columns:
#> id dadid momid sex famid steril
#> col_class <character> <character> <character> <ordered> <character> <logical>
#> 1_103 1_103 <NA> <NA> male 1 <NA>
#> 1_104 1_104 <NA> <NA> female 1 <NA>
#> 1_105 1_105 <NA> <NA> male 1 <NA>
#> 1_106 1_106 <NA> <NA> female 1 <NA>
#> 1_109 1_109 <NA> <NA> female 1 <NA>
#> ... ... ... ... ... ... ...
#> 1_118 1_118 1_105 1_106 female 1 <NA>
#> 1_119 1_119 1_105 1_106 male 1 <NA>
#> 1_124 1_124 1_110 1_109 male 1 <NA>
#> 1_127 1_127 1_114 1_115 male 1 <NA>
#> 1_128 1_128 1_114 1_115 male 1 <NA>
#> status avail affected useful kin isinf
#> col_class <logical> <logical> <logical> <logical> <numeric> <logical>
#> 1_103 <NA> FALSE TRUE <NA> <NA> <NA>
#> 1_104 <NA> FALSE FALSE <NA> <NA> <NA>
#> 1_105 <NA> FALSE <NA> <NA> <NA> <NA>
#> 1_106 <NA> FALSE <NA> <NA> <NA> <NA>
#> 1_109 <NA> TRUE FALSE <NA> <NA> <NA>
#> ... ... ... ... ... ... ...
#> 1_118 <NA> TRUE TRUE <NA> <NA> <NA>
#> 1_119 <NA> TRUE TRUE <NA> <NA> <NA>
#> 1_124 <NA> TRUE TRUE <NA> <NA> <NA>
#> 1_127 <NA> TRUE TRUE <NA> <NA> <NA>
#> 1_128 <NA> TRUE TRUE <NA> <NA> <NA>
#> num_child_tot num_child_dir num_child_ind | family indId
#> col_class <numeric> <numeric> <numeric> <character> <character>
#> 1_103 2 2 0 1 103
#> 1_104 2 2 0 1 104
#> 1_105 3 3 0 1 105
#> 1_106 3 3 0 1 106
#> 1_109 1 1 0 1 109
#> ... ... ... ... ... ...
#> 1_118 0 0 0 1 118
#> 1_119 0 0 0 1 119
#> 1_124 0 0 0 1 124
#> 1_127 0 0 0 1 127
#> 1_128 0 0 0 1 128
#> fatherId motherId gender affection available
#> col_class <character> <character> <character> <character> <character>
#> 1_103 135 136 1 1 0
#> 1_104 <NA> <NA> 2 0 0
#> 1_105 <NA> <NA> 1 <NA> 0
#> 1_106 <NA> <NA> 2 <NA> 0
#> 1_109 101 102 2 0 1
#> ... ... ... ... ... ...
#> 1_118 105 106 2 1 1
#> 1_119 105 106 1 1 1
#> 1_124 110 109 1 1 1
#> 1_127 114 115 1 1 1
#> 1_128 114 115 1 1 1
#> num error sterilisation vitalStatus affection_mods
#> col_class <character> <character> <character> <character> <character>
#> 1_103 2 <NA> <NA> <NA> 1
#> 1_104 4 <NA> <NA> <NA> 0
#> 1_105 6 <NA> <NA> <NA> NA
#> 1_106 1 <NA> <NA> <NA> NA
#> 1_109 3 <NA> <NA> <NA> 0
#> ... ... ... ... ... ...
#> 1_118 2 <NA> <NA> <NA> 1
#> 1_119 6 <NA> <NA> <NA> 1
#> 1_124 <NA> <NA> <NA> <NA> 1
#> 1_127 5 <NA> <NA> <NA> 1
#> 1_128 3 <NA> <NA> <NA> 1
#> avail_mods
#> col_class <character>
#> 1_103 0
#> 1_104 0
#> 1_105 0
#> 1_106 0
#> 1_109 1
#> ... ...
#> 1_118 1
#> 1_119 1
#> 1_124 1
#> 1_127 1
#> 1_128 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>
#>
#> $id_trim
#>
#> "1_101" "1_102" "1_107" "1_108" "1_111" "1_113" "1_121" "1_122" "1_123" "1_131"
#> id
#> "1_132" "1_134" "1_139" "1_141" "1_140" "1_130" "1_126" "1_125" "1_129" "1_133"
#>
#> "1_116"
#>
#> $id_lst
#> $id_lst$unavail
#> [1] "1_101" "1_102" "1_107" "1_108" "1_111" "1_113" "1_121" "1_122" "1_123"
#> [10] "1_131" "1_132" "1_134" "1_139"
#>
#> $id_lst$affect
#> id
#> "1_141" "1_140" "1_130" "1_126" "1_125" "1_129" "1_133" "1_116"
#>
#>
#> $bit_size
#> [1] 46 29 27 23 21 19 15 14 13 11
#>
#> $avail
#> [1] FALSE FALSE FALSE FALSE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE
#> [13] TRUE
#>
#> $pedSizeOriginal
#> [1] 41
#>
#> $pedSizeIntermed
#> [1] 28
#>
#> $pedSizeFinal
#> [1] 13
#>