There are several by-locus summary functions available for gtypes objects. Given some sample microsatellite data:
data(msats.g)
msats <- stratify(msats.g, "broad")
msats <- msats[, locNames(msats)[1:4], ]
One can calculate the following summaries:
The number of alleles at each locus:
numAlleles(msats)
## D11t EV37 EV94 Ttr11
## 12 22 15 9
The number of samples with missing data at each locus:
numMissing(msats)
## D11t EV37 EV94 Ttr11
## 1 7 1 1
which can also be expressed as a proportion of samples with missing data:
numMissing(msats, prop = TRUE)
## D11t EV37 EV94 Ttr11
## 0.0079 0.0556 0.0079 0.0079
The allelic richness, or the average number of alleles per sample:
allelicRichness(msats)
## D11t EV37 EV94 Ttr11
## 0.096 0.185 0.120 0.072
The observed and expected heterozygosity:
obsvdHet(msats)
## D11t EV37 EV94 Ttr11
## 0.70 0.70 0.78 0.70
exptdHet(msats)
## D11t EV37 EV94 Ttr11
## 0.75 0.83 0.83 0.80
The proportion of alleles that are unique (present in only one sample):
propUniqueAlleles(msats)
## D11t EV37 EV94 Ttr11
## 0.250 0.136 0.067 0.222
The value of theta based on heterozygosity:
theta(msats)
## D11t EV37 EV94 Ttr11
## 0.56 0.62 0.62 0.59
These measures are all calculated in the summarizeLoci function and returned as a matrix. This function also allows you to calculate the measures for each stratum separately, which returns a list for each stratum:
summarizeLoci(msats)
## num.genotyped prop.genotyped num.alleles allelic.richness
## D11t 125 0.99 12 0.096
## EV37 119 0.94 22 0.185
## EV94 125 0.99 15 0.120
## Ttr11 125 0.99 9 0.072
## prop.unique.alleles exptd.heterozygosity obsvd.heterozygosity
## D11t 0.250 0.75 0.70
## EV37 0.136 0.83 0.70
## EV94 0.067 0.83 0.78
## Ttr11 0.222 0.80 0.70
summarizeLoci(msats, by.strata = TRUE)
## $Coastal
## num.genotyped prop.genotyped num.alleles allelic.richness
## D11t 67 0.99 3 0.045
## EV37 63 0.93 7 0.111
## EV94 68 1.00 5 0.074
## Ttr11 68 1.00 4 0.059
## prop.unique.alleles exptd.heterozygosity obsvd.heterozygosity
## D11t 0.00 0.49 0.52
## EV37 0.43 0.61 0.62
## EV94 0.00 0.77 0.74
## Ttr11 0.00 0.66 0.63
##
## $Offshore
## num.genotyped prop.genotyped num.alleles allelic.richness
## D11t 58 1.00 12 0.21
## EV37 56 0.97 22 0.39
## EV94 57 0.98 15 0.26
## Ttr11 57 0.98 9 0.16
## prop.unique.alleles exptd.heterozygosity obsvd.heterozygosity
## D11t 0.250 0.86 0.91
## EV37 0.136 0.94 0.79
## EV94 0.067 0.86 0.82
## Ttr11 0.222 0.82 0.79
One can also obtain the allelic frequencies for each locus overall and by-strata by:
alleleFreqs(msats)
## $D11t
## freq prop
## 117 1 0.004
## 119 1 0.004
## 121 4 0.016
## 127 1 0.004
## 129 3 0.012
## 131 16 0.064
## 133 75 0.300
## 135 96 0.384
## 137 20 0.080
## 139 20 0.080
## 141 7 0.028
## 143 6 0.024
##
## $EV37
## freq prop
## 190 3 0.0126
## 200 4 0.0168
## 202 5 0.0210
## 204 2 0.0084
## 206 7 0.0294
## 208 8 0.0336
## 210 3 0.0126
## 212 13 0.0546
## 214 86 0.3613
## 216 39 0.1639
## 218 8 0.0336
## 220 6 0.0252
## 222 20 0.0840
## 224 11 0.0462
## 226 3 0.0126
## 228 8 0.0336
## 230 5 0.0210
## 232 2 0.0084
## 234 1 0.0042
## 236 2 0.0084
## 240 1 0.0042
## 254 1 0.0042
##
## $EV94
## freq prop
## 229 1 0.004
## 239 2 0.008
## 243 15 0.060
## 245 18 0.072
## 247 3 0.012
## 249 83 0.332
## 251 41 0.164
## 253 7 0.028
## 255 6 0.024
## 259 27 0.108
## 261 27 0.108
## 263 7 0.028
## 265 8 0.032
## 269 3 0.012
## 271 2 0.008
##
## $Ttr11
## freq prop
## 193 1 0.004
## 197 10 0.040
## 207 53 0.212
## 209 17 0.068
## 211 35 0.140
## 213 80 0.320
## 215 46 0.184
## 217 7 0.028
## 219 1 0.004
alleleFreqs(msats, by.strata = TRUE)
## $D11t
## , , Coastal
##
## freq prop
## 117 0 0.000
## 119 0 0.000
## 121 0 0.000
## 127 0 0.000
## 129 0 0.000
## 131 0 0.000
## 133 48 0.358
## 135 83 0.619
## 137 3 0.022
## 139 0 0.000
## 141 0 0.000
## 143 0 0.000
##
## , , Offshore
##
## freq prop
## 117 1 0.0086
## 119 1 0.0086
## 121 4 0.0345
## 127 1 0.0086
## 129 3 0.0259
## 131 16 0.1379
## 133 27 0.2328
## 135 13 0.1121
## 137 17 0.1466
## 139 20 0.1724
## 141 7 0.0603
## 143 6 0.0517
##
##
## $EV37
## , , Coastal
##
## freq prop
## 190 0 0.0000
## 200 0 0.0000
## 202 0 0.0000
## 204 0 0.0000
## 206 0 0.0000
## 208 0 0.0000
## 210 0 0.0000
## 212 1 0.0079
## 214 71 0.5635
## 216 33 0.2619
## 218 2 0.0159
## 220 0 0.0000
## 222 11 0.0873
## 224 7 0.0556
## 226 1 0.0079
## 228 0 0.0000
## 230 0 0.0000
## 232 0 0.0000
## 234 0 0.0000
## 236 0 0.0000
## 240 0 0.0000
## 254 0 0.0000
##
## , , Offshore
##
## freq prop
## 190 3 0.0268
## 200 4 0.0357
## 202 5 0.0446
## 204 2 0.0179
## 206 7 0.0625
## 208 8 0.0714
## 210 3 0.0268
## 212 12 0.1071
## 214 15 0.1339
## 216 6 0.0536
## 218 6 0.0536
## 220 6 0.0536
## 222 9 0.0804
## 224 4 0.0357
## 226 2 0.0179
## 228 8 0.0714
## 230 5 0.0446
## 232 2 0.0179
## 234 1 0.0089
## 236 2 0.0179
## 240 1 0.0089
## 254 1 0.0089
##
##
## $EV94
## , , Coastal
##
## freq prop
## 229 0 0.000
## 239 0 0.000
## 243 0 0.000
## 245 12 0.088
## 247 0 0.000
## 249 47 0.346
## 251 30 0.221
## 253 0 0.000
## 255 0 0.000
## 259 25 0.184
## 261 22 0.162
## 263 0 0.000
## 265 0 0.000
## 269 0 0.000
## 271 0 0.000
##
## , , Offshore
##
## freq prop
## 229 1 0.0088
## 239 2 0.0175
## 243 15 0.1316
## 245 6 0.0526
## 247 3 0.0263
## 249 36 0.3158
## 251 11 0.0965
## 253 7 0.0614
## 255 6 0.0526
## 259 2 0.0175
## 261 5 0.0439
## 263 7 0.0614
## 265 8 0.0702
## 269 3 0.0263
## 271 2 0.0175
##
##
## $Ttr11
## , , Coastal
##
## freq prop
## 193 0 0.000
## 197 0 0.000
## 207 42 0.309
## 209 0 0.000
## 211 0 0.000
## 213 59 0.434
## 215 33 0.243
## 217 2 0.015
## 219 0 0.000
##
## , , Offshore
##
## freq prop
## 193 1 0.0088
## 197 10 0.0877
## 207 11 0.0965
## 209 17 0.1491
## 211 35 0.3070
## 213 21 0.1842
## 215 13 0.1140
## 217 5 0.0439
## 219 1 0.0088