as.genclone will create a genclone object from a genind object OR anything that can be passed to the genind initializer.
bootgen2genind(bg) as.genclone(x, ..., mlg, mlgclass = TRUE) genclone2genind(x) as.genambig(x)
bg | a bootgen object |
---|---|
x | a |
... | arguments passed on to the |
mlg | an optional vector of multilocus genotypes as integers |
mlgclass | should the mlg slot be of class MLG? |
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.
splitStrata
, genclone
,
read.genalex
aboot
#> /// 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) }#>#> 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: NAdata(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 -