as.genclone will create a genclone object from a genind object OR anything that can be passed to the genind initializer.
Usage
bootgen2genind(bg)
as.genclone(x, ..., mlg, mlgclass = TRUE)
genclone2genind(x)
as.genambig(x)Details
genclone2genind will remove the mlg slot from the genclone object, creating a genind object.
as.genambig will convert a genind or genclone object to a polysat genambig class.
Examples
data(Aeut)
Aeut
#> /// GENIND OBJECT /////////
#>
#> // 187 individuals; 56 loci; 56 alleles; size: 68.9 Kb
#>
#> // Basic content
#> @tab: 187 x 56 matrix of allele counts
#> @loc.n.all: number of alleles per locus (range: 56-56)
#> @ploidy: ploidy of each individual (range: 2-2)
#> @type: PA
#> @call: old2new_genind(object = x, donor = new(class(x)))
#>
#> // Optional content
#> @pop: population of each individual (group size range: 90-97)
#> @other: a list containing: population_hierarchy
#>
# Conversion to genclone --------------------------------------------------
Aeut.gc <- as.genclone(Aeut)
Aeut.gc
#>
#> This is a genclone object
#> -------------------------
#> Genotype information:
#>
#> 119 original multilocus genotypes
#> 187 diploid individuals
#> 56 dominant loci
#>
#> Population information:
#>
#> 0 strata.
#> 2 populations defined - Athena, Mt. Vernon
# Conversion to genind ----------------------------------------------------
Aeut.gi <- genclone2genind(Aeut.gc)
Aeut.gi
#> /// GENIND OBJECT /////////
#>
#> // 187 individuals; 56 loci; 56 alleles; size: 68.2 Kb
#>
#> // Basic content
#> @tab: 187 x 56 matrix of allele counts
#> @loc.n.all: number of alleles per locus (range: 56-56)
#> @ploidy: ploidy of each individual (range: 2-2)
#> @type: PA
#> @call: genclone2genind(x = Aeut.gc)
#>
#> // Optional content
#> @pop: population of each individual (group size range: 90-97)
#> @other: a list containing: population_hierarchy
#>
# Conversion to polysat's "genambig" class --------------------------------
if (require("polysat")) {
data(Pinf)
Pinf.gb <- as.genambig(Pinf)
summary(Pinf.gb)
}
#> Loading required package: polysat
#> Dataset with allele copy number ambiguity.
#> Insert dataset description here.
#> Number of missing genotypes: 10
#> 86 samples, 11 loci.
#> 2 populations.
#> Ploidies: 2 3 NA
#> Length(s) of microsatellite repeats: NA
data(nancycats)
# Conversion to bootgen for random sampling of loci -----------------------
nan.bg <- new("bootgen", nancycats[pop = 9])
nan.bg
#> An object of class "bootgen"
#> Slot "type":
#> [1] "codom"
#>
#> Slot "ploidy":
#> [1] 2 2 2 2 2 2 2 2 2
#>
#> Slot "names":
#> [1] "N104" "N105" "N106" "N107" "N108" "N109" "N111" "N112" "N113"
#>
#> Slot "alllist":
#> [[1]]
#> [1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
#>
#> [[2]]
#> [1] 17 18 19 20 21 22 23 24 25 26 27
#>
#> [[3]]
#> [1] 28 29 30 31 32 33 34 35 36 37
#>
#> [[4]]
#> [1] 38 39 40 41 42 43 44 45 46
#>
#> [[5]]
#> [1] 47 48 49 50 51 52 53 54 55 56 57 58
#>
#> [[6]]
#> [1] 59 60 61 62 63 64 65 66
#>
#> [[7]]
#> [1] 67 68 69 70 71 72 73 74 75 76 77 78
#>
#> [[8]]
#> [1] 79 80 81 82 83 84 85 86 87 88 89 90
#>
#> [[9]]
#> [1] 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108
#>
#>
#> Slot "tab":
#> fca8.117 fca8.119 fca8.121 fca8.123 fca8.127 fca8.129 fca8.131 fca8.133
#> N104 0 0 0.5 0.0 0 0 0 0
#> N105 0 0 0.0 0.0 0 0 0 0
#> N106 0 0 0.0 0.0 0 0 0 0
#> N107 0 0 0.5 0.0 0 0 0 0
#> N108 0 0 0.0 0.0 0 0 0 0
#> N109 0 0 0.0 0.0 0 0 0 0
#> N111 0 0 0.0 0.0 0 0 0 0
#> N112 0 0 0.5 0.0 0 0 0 0
#> N113 0 0 0.0 0.5 0 0 0 0
#> fca8.135 fca8.137 fca8.139 fca8.141 fca8.143 fca8.145 fca8.147 fca8.149
#> N104 0.5 0.0 0 0 0 0 0 0
#> N105 0.0 1.0 0 0 0 0 0 0
#> N106 1.0 0.0 0 0 0 0 0 0
#> N107 0.5 0.0 0 0 0 0 0 0
#> N108 1.0 0.0 0 0 0 0 0 0
#> N109 0.0 1.0 0 0 0 0 0 0
#> N111 1.0 0.0 0 0 0 0 0 0
#> N112 0.0 0.5 0 0 0 0 0 0
#> N113 0.0 0.5 0 0 0 0 0 0
#> fca23.128 fca23.130 fca23.132 fca23.136 fca23.138 fca23.140 fca23.142
#> N104 0 0 0.0 0.5 0.0 0.5 0.0
#> N105 0 0 0.0 0.5 0.0 0.5 0.0
#> N106 0 0 0.5 0.5 0.0 0.0 0.0
#> N107 0 0 0.5 0.5 0.0 0.0 0.0
#> N108 0 0 0.5 0.5 0.0 0.0 0.0
#> N109 0 0 0.0 0.5 0.0 0.5 0.0
#> N111 0 0 0.0 0.0 0.5 0.0 0.0
#> N112 0 0 0.5 0.5 0.0 0.0 0.0
#> N113 0 0 0.0 0.5 0.0 0.0 0.5
#> fca23.144 fca23.146 fca23.148 fca23.150 fca43.133 fca43.135 fca43.137
#> N104 0 0.0 0 0 0 0 0
#> N105 0 0.0 0 0 0 0 0
#> N106 0 0.0 0 0 0 0 0
#> N107 0 0.0 0 0 0 0 0
#> N108 0 0.0 0 0 0 0 0
#> N109 0 0.0 0 0 0 0 0
#> N111 0 0.5 0 0 0 0 0
#> N112 0 0.0 0 0 0 0 0
#> N113 0 0.0 0 0 0 0 0
#> fca43.139 fca43.141 fca43.143 fca43.145 fca43.147 fca43.149 fca43.157
#> N104 1.0 0.0 0 0.0 0 0 0
#> N105 0.0 0.0 0 1.0 0 0 0
#> N106 0.5 0.0 0 0.5 0 0 0
#> N107 0.5 0.0 0 0.5 0 0 0
#> N108 0.5 0.0 0 0.5 0 0 0
#> N109 0.5 0.0 0 0.5 0 0 0
#> N111 1.0 0.0 0 0.0 0 0 0
#> N112 0.0 0.5 0 0.5 0 0 0
#> N113 1.0 0.0 0 0.0 0 0 0
#> fca45.116 fca45.118 fca45.120 fca45.122 fca45.126 fca45.128 fca45.130
#> N104 0.0 0.0 0.0 0.0 0.0 1.0 0.0
#> N105 0.0 0.0 0.5 0.0 0.5 0.0 0.0
#> N106 0.0 0.0 0.0 0.5 0.5 0.0 0.0
#> N107 0.0 0.0 0.0 0.5 0.0 0.5 0.0
#> N108 0.0 0.0 0.0 0.5 0.0 0.5 0.0
#> N109 0.0 0.0 0.5 0.0 0.5 0.0 0.0
#> N111 0.0 0.0 0.0 0.5 0.0 0.0 0.0
#> N112 0.0 0.0 0.0 0.5 0.0 0.0 0.5
#> N113 0.5 0.5 0.0 0.0 0.0 0.0 0.0
#> fca45.132 fca45.134 fca77.132 fca77.142 fca77.144 fca77.146 fca77.148
#> N104 0.0 0 0 0 0.0 0 0
#> N105 0.0 0 0 0 0.0 0 0
#> N106 0.0 0 0 0 0.0 0 0
#> N107 0.0 0 0 0 0.0 0 0
#> N108 0.0 0 0 0 0.0 0 0
#> N109 0.0 0 0 0 0.5 0 0
#> N111 0.5 0 0 0 0.0 0 0
#> N112 0.0 0 0 0 0.0 0 0
#> N113 0.0 0 0 0 0.0 0 0
#> fca77.150 fca77.152 fca77.154 fca77.156 fca77.158 fca77.160 fca77.162
#> N104 0.5 0 0.5 0.0 0.0 0 0
#> N105 1.0 0 0.0 0.0 0.0 0 0
#> N106 0.5 0 0.0 0.5 0.0 0 0
#> N107 0.5 0 0.5 0.0 0.0 0 0
#> N108 0.5 0 0.0 0.0 0.5 0 0
#> N109 0.5 0 0.0 0.0 0.0 0 0
#> N111 0.0 0 0.0 0.0 1.0 0 0
#> N112 1.0 0 0.0 0.0 0.0 0 0
#> N113 0.0 0 0.0 0.0 1.0 0 0
#> fca78.138 fca78.140 fca78.142 fca78.144 fca78.146 fca78.148 fca78.150
#> N104 0 0 0.5 0 0 0.0 0.5
#> N105 0 0 0.5 0 0 0.0 0.5
#> N106 0 0 0.5 0 0 0.0 0.5
#> N107 0 0 0.5 0 0 0.0 0.5
#> N108 0 0 0.5 0 0 0.0 0.5
#> N109 0 0 0.5 0 0 0.0 0.5
#> N111 0 0 1.0 0 0 0.0 0.0
#> N112 0 0 0.5 0 0 0.0 0.5
#> N113 0 0 0.5 0 0 0.5 0.0
#> fca78.152 fca90.181 fca90.185 fca90.187 fca90.189 fca90.191 fca90.193
#> N104 0 0 0.0 0.5 0 0 0.0
#> N105 0 0 0.0 0.0 0 0 0.0
#> N106 0 0 0.0 0.5 0 0 0.0
#> N107 0 0 0.0 0.5 0 0 0.0
#> N108 0 0 0.0 0.0 0 0 0.5
#> N109 0 0 0.0 0.5 0 0 0.0
#> N111 0 0 0.5 0.0 0 0 0.0
#> N112 0 0 0.0 0.0 0 0 0.5
#> N113 0 0 0.0 0.0 0 0 0.0
#> fca90.195 fca90.197 fca90.199 fca90.201 fca90.203 fca90.205 fca96.091
#> N104 0 0 0.5 0.0 0 0 0.0
#> N105 0 0 1.0 0.0 0 0 0.0
#> N106 0 0 0.5 0.0 0 0 0.0
#> N107 0 0 0.5 0.0 0 0 0.0
#> N108 0 0 0.5 0.0 0 0 0.0
#> N109 0 0 0.5 0.0 0 0 0.0
#> N111 0 0 0.0 0.5 0 0 0.5
#> N112 0 0 0.5 0.0 0 0 0.0
#> N113 0 0 1.0 0.0 0 0 0.5
#> fca96.101 fca96.103 fca96.105 fca96.107 fca96.109 fca96.111 fca96.113
#> N104 0.0 0.5 0 0 0 0 0.5
#> N105 0.5 0.5 0 0 0 0 0.0
#> N106 0.5 0.0 0 0 0 0 0.5
#> N107 0.0 0.5 0 0 0 0 0.5
#> N108 0.0 0.5 0 0 0 0 0.5
#> N109 0.0 0.5 0 0 0 0 0.0
#> N111 0.0 0.0 0 0 0 0 0.5
#> N112 0.0 1.0 0 0 0 0 0.0
#> N113 0.5 0.0 0 0 0 0 0.0
#> fca96.115 fca96.117 fca96.119 fca96.121 fca37.182 fca37.184 fca37.186
#> N104 0.0 0 0 0 0.0 0 0
#> N105 0.0 0 0 0 1.0 0 0
#> N106 0.0 0 0 0 0.5 0 0
#> N107 0.0 0 0 0 0.5 0 0
#> N108 0.0 0 0 0 0.0 0 0
#> N109 0.5 0 0 0 0.5 0 0
#> N111 0.0 0 0 0 0.0 0 0
#> N112 0.0 0 0 0 0.5 0 0
#> N113 0.0 0 0 0 0.0 0 0
#> fca37.192 fca37.194 fca37.200 fca37.202 fca37.204 fca37.206 fca37.208
#> N104 0 0 0 0 0 0.0 1.0
#> N105 0 0 0 0 0 0.0 0.0
#> N106 0 0 0 0 0 0.0 0.5
#> N107 0 0 0 0 0 0.0 0.5
#> N108 0 0 0 0 0 0.0 1.0
#> N109 0 0 0 0 0 0.0 0.5
#> N111 0 0 0 0 0 0.0 0.5
#> N112 0 0 0 0 0 0.5 0.0
#> N113 0 0 0 0 0 0.0 0.5
#> fca37.210 fca37.212 fca37.214 fca37.216 fca37.218 fca37.220 fca37.224
#> N104 0 0 0.0 0 0 0 0
#> N105 0 0 0.0 0 0 0 0
#> N106 0 0 0.0 0 0 0 0
#> N107 0 0 0.0 0 0 0 0
#> N108 0 0 0.0 0 0 0 0
#> N109 0 0 0.0 0 0 0 0
#> N111 0 0 0.5 0 0 0 0
#> N112 0 0 0.0 0 0 0 0
#> N113 0 0 0.5 0 0 0 0
#> fca37.226
#> N104 0
#> N105 0
#> N106 0
#> N107 0
#> N108 0
#> N109 0
#> N111 0
#> N112 0
#> N113 0
#>
#> Slot "loc.fac":
#> [1] fca8 fca8 fca8 fca8 fca8 fca8 fca8 fca8 fca8 fca8 fca8 fca8
#> [13] fca8 fca8 fca8 fca8 fca23 fca23 fca23 fca23 fca23 fca23 fca23 fca23
#> [25] fca23 fca23 fca23 fca43 fca43 fca43 fca43 fca43 fca43 fca43 fca43 fca43
#> [37] fca43 fca45 fca45 fca45 fca45 fca45 fca45 fca45 fca45 fca45 fca77 fca77
#> [49] fca77 fca77 fca77 fca77 fca77 fca77 fca77 fca77 fca77 fca77 fca78 fca78
#> [61] fca78 fca78 fca78 fca78 fca78 fca78 fca90 fca90 fca90 fca90 fca90 fca90
#> [73] fca90 fca90 fca90 fca90 fca90 fca90 fca96 fca96 fca96 fca96 fca96 fca96
#> [85] fca96 fca96 fca96 fca96 fca96 fca96 fca37 fca37 fca37 fca37 fca37 fca37
#> [97] fca37 fca37 fca37 fca37 fca37 fca37 fca37 fca37 fca37 fca37 fca37 fca37
#> Levels: fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
#>
#> Slot "loc.n.all":
#> fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 fca37
#> 16 11 10 9 12 8 12 12 18
#>
#> Slot "all.names":
#> $fca8
#> [1] "117" "119" "121" "123" "127" "129" "131" "133" "135" "137" "139" "141"
#> [13] "143" "145" "147" "149"
#>
#> $fca23
#> [1] "128" "130" "132" "136" "138" "140" "142" "144" "146" "148" "150"
#>
#> $fca43
#> [1] "133" "135" "137" "139" "141" "143" "145" "147" "149" "157"
#>
#> $fca45
#> [1] "116" "118" "120" "122" "126" "128" "130" "132" "134"
#>
#> $fca77
#> [1] "132" "142" "144" "146" "148" "150" "152" "154" "156" "158" "160" "162"
#>
#> $fca78
#> [1] "138" "140" "142" "144" "146" "148" "150" "152"
#>
#> $fca90
#> [1] "181" "185" "187" "189" "191" "193" "195" "197" "199" "201" "203" "205"
#>
#> $fca96
#> [1] "091" "101" "103" "105" "107" "109" "111" "113" "115" "117" "119" "121"
#>
#> $fca37
#> [1] "182" "184" "186" "192" "194" "200" "202" "204" "206" "208" "210" "212"
#> [13] "214" "216" "218" "220" "224" "226"
#>
#>
#> Slot "other":
#> NULL
#>
#> Slot "call":
#> NULL
#>
# Conversion back to genind -----------------------------------------------
nan.gid <- bootgen2genind(nan.bg)
nan.gid
#> /// GENIND OBJECT /////////
#>
#> // 9 individuals; 9 loci; 108 alleles; size: 25.7 Kb
#>
#> // Basic content
#> @tab: 9 x 108 matrix of allele counts
#> @loc.n.all: number of alleles per locus (range: 8-18)
#> @loc.fac: locus factor for the 108 columns of @tab
#> @all.names: list of allele names for each locus
#> @ploidy: ploidy of each individual (range: 2-2)
#> @type: codom
#> @call: .local(.Object = .Object, tab = ..1)
#>
#> // Optional content
#> - empty -