GenotypeUtils.jl
PopGenCore.jl/src/Utils/GenotypeUtils.jl
| 📦 not exported | 🟪 exported by PopGenCore.jl | 🔵 exported by PopGen.jl |
|---|
🟪 alleles
allelecount(locus::T) where T<:GenoArray
Return the number of unique alleles present at a locus.
🟪 alleles
alleles(locus::T) where T<:GenoArray
Return an array of all the non-missing alleles of a locus.
🟪 alleles
alleles(locus::T, miss::Bool = false) where T<:GenoArray
Return an array of all the non-missing alleles of a locus. Use the second positional
argument as true to include missing values.
🟪 uniquealleles
uniquealleles(locus::T) where T<:GenoArray
Return an array of all the unique non-missing alleles of a locus.
🟪 locidataframe
locidataframe(data::PopData)
Return a wide DataFrame of samples as columns, ommitting population information.
Example
julia> locidataframe(@nancycats)
9×237 DataFrame. Omitted printing of 232 columns
│ Row │ N215 │ N216 │ N217 │ N218 │ N219 │
│ │ Tuple…? │ Tuple…? │ Tuple…? │ Tuple…? │ Tuple…? │
├─────┼────────────┼────────────┼────────────┼────────────┼────────────┤
│ 1 │ missing │ missing │ (135, 143) │ (133, 135) │ (133, 135) │
│ 2 │ (136, 146) │ (146, 146) │ (136, 146) │ (138, 138) │ (140, 146) │
│ 3 │ (139, 139) │ (139, 145) │ (141, 141) │ (139, 141) │ (141, 145) │
│ 4 │ (116, 120) │ (120, 126) │ (116, 116) │ (116, 126) │ (126, 126) │
│ 5 │ (156, 156) │ (156, 156) │ (152, 156) │ (150, 150) │ (152, 152) │
│ 6 │ (142, 148) │ (142, 148) │ (142, 142) │ (142, 148) │ (142, 148) │
│ 7 │ (199, 199) │ (185, 199) │ (197, 197) │ (199, 199) │ (193, 199) │
│ 8 │ (113, 113) │ (113, 113) │ (113, 113) │ (91, 105) │ (113, 113) │
│ 9 │ (208, 208) │ (208, 208) │ (210, 210) │ (208, 208) │ (208, 208) │
🟪 locimatrix
locimatrix(data::PopData)
Return a matrix of genotypes with dimensions samples × loci.
Rows are samples and columns are loci. Will return an error if ploidy varies between samples.
Example
julia> locimatrix(@nancycats)
237×9 Array{Union{Missing, Tuple{Int16,Int16}},2}:
missing (136, 146) (139, 139) … (199, 199) (113, 113) (208, 208)
missing (146, 146) (139, 145) (185, 199) (113, 113) (208, 208)
(135, 143) (136, 146) (141, 141) (197, 197) (113, 113) (210, 210)
(133, 135) (138, 138) (139, 141) (199, 199) (91, 105) (208, 208)
(133, 135) (140, 146) (141, 145) (193, 199) (113, 113) (208, 208)
(135, 143) (136, 146) (145, 149) … (193, 195) (91, 113) (208, 208)
(135, 135) (136, 146) (139, 145) (199, 199) (105, 113) (208, 208)
(135, 143) (136, 146) (135, 149) (193, 197) (91, 91) (208, 212)
(137, 143) (136, 146) (139, 139) (197, 197) (105, 113) (208, 212)
(135, 135) (132, 132) (141, 145) (197, 197) (91, 105) (208, 208)
(137, 141) (130, 136) (137, 145) … (193, 199) (91, 91) (182, 182)
(129, 133) (130, 136) (135, 145) (193, 199) (91, 113) (182, 208)
⋮ ⋱
(133, 135) (136, 136) (135, 139) … (199, 199) (113, 113) (182, 182)
(133, 141) (136, 136) (135, 139) (197, 197) (113, 113) (182, 208)
(133, 141) (130, 146) (141, 141) (191, 199) missing (208, 208)
(123, 133) (138, 138) (141, 145) (191, 197) missing (208, 208)
(123, 133) (138, 138) (139, 139) (197, 199) missing (208, 208)
(133, 141) (136, 146) (139, 139) … (197, 197) missing (208, 208)
(133, 141) (130, 136) (139, 145) (191, 199) missing (208, 208)
(133, 141) (136, 146) (139, 145) (199, 199) missing (208, 220)
(133, 143) (130, 130) (135, 145) (197, 197) missing (208, 208)
(135, 141) (136, 144) (143, 143) (191, 197) (113, 117) (208, 208)
(137, 143) (130, 136) (135, 145) … (193, 199) (113, 117) (208, 208)
(135, 141) (130, 146) (135, 139) (197, 197) missing (208, 208)
🟪 phasedmatrix
phasedmatrix(data::PopData)
Return a Vector of length ploidy composed of allele matrices with dimensions samples × loci.
Rows are samples and columns are loci. Will return an error if ploidy varies between samples.
Example
julia> mtx = phasedmatrix(@nancycats)
2-element Array{Array{Union{Missing, Int16},2},1}:
[missing 136 … 113 208; missing 146 … 113 208; … ; 137 130 … 113 208; 135 130 … missing 208]
[missing 146 … 113 208; missing 146 … 113 208; … ; 143 136 … 117 208; 141 146 … missing 208]
julia> mtx[1]
237×9 Array{Union{Missing, Int16},2}:
missing 136 139 116 156 142 199 113 208
missing 146 139 120 156 142 185 113 208
135 136 141 116 152 142 197 113 210
133 138 139 116 150 142 199 91 208
133 140 141 126 152 142 193 113 208
135 136 145 120 150 148 193 91 208
135 136 139 116 152 142 199 105 208
135 136 135 120 154 142 193 91 208
137 136 139 116 150 142 197 105 208
135 132 141 120 150 148 197 91 208
137 130 137 128 152 142 193 91 182
129 130 135 126 144 140 193 91 182
⋮ ⋮
133 136 135 missing 146 142 199 113 182
133 136 135 missing 150 142 197 113 182
133 130 141 missing 148 142 191 missing 208
123 138 141 missing 148 142 191 missing 208
123 138 139 missing 150 142 197 missing 208
133 136 139 missing 150 142 197 missing 208
133 130 139 missing 152 142 191 missing 208
133 136 139 missing 150 142 199 missing 208
133 130 135 missing 148 142 197 missing 208
135 136 143 missing 144 142 191 113 208
137 130 135 missing 150 142 193 113 208
135 130 135 missing 150 142 197 missing 208