genclone
or
genind
object independently over each locus.R/sample_schemes.r
shufflepop.Rd
Shuffle individuals in a genclone
or
genind
object independently over each locus.
shufflepop(pop, method = 1)
pop | a |
---|---|
method | an integer between 1 and 4. See details below. |
a genclone
or genind
object
shuffled by a specified method
This function will shuffle each locus in the data set independently of one another, rendering them essentially unlinked. The following methods are available to shuffle your data:
Permute Alleles This will redistribute all alleles in the sample throughout the locus. Missing data is fixed in place. This maintains allelic structure, but heterozygosity is variable.
Parametric Bootstrap This will redistribute available alleles within the locus based on their allelic frequencies. This means that both the allelic state and heterozygosity will vary. The resulting data set will not have missing data.
Non-Parametric Bootstrap This will shuffle the allelic state for each individual. Missing data is fixed in place.
Multilocus Style Permutation This will shuffle the genotypes at each locus, maintaining the heterozygosity and allelic structure.
Paul-Michael Agapow and Austin Burt. 2001. Indices of multilocus linkage disequilibrium. Molecular Ecology Notes, 1(1-2):101-102
# load the microbov dataset data(microbov) # Let's look at a single population for now. Howsabout Zebu Zebu <- popsub(microbov, "Zebu") summary(Zebu)#> #> // Number of individuals: 50 #> // Group sizes: 50 #> // Number of alleles per locus: 7 6 8 5 7 6 5 5 9 6 10 9 10 9 9 5 5 10 9 9 11 8 10 8 6 8 8 8 13 6 #> // Number of alleles per group: 235 #> // Percentage of missing data: 0.87 % #> // Observed heterozygosity: 0.54 0.58 0.7 0.67 0.48 0.6 0.46 0.5 0.71 0.8 0.74 0.86 0.78 0.72 0.9 0.82 0.62 0.74 0.82 0.64 0.8 0.41 0.6 0.76 0.58 0.52 0.76 0.66 0.82 0.4 #> // Expected heterozygosity: 0.71 0.61 0.74 0.73 0.75 0.64 0.58 0.6 0.66 0.76 0.81 0.83 0.75 0.78 0.82 0.76 0.59 0.78 0.83 0.63 0.82 0.42 0.8 0.8 0.73 0.61 0.74 0.65 0.83 0.44# Take note of the Number of alleles per population and the Observed # heterozygosity as we go through each method. # Permute Alleles: maintain allelic state; heterozygosity varies. summary(shufflepop(Zebu, method=1))#> #> // Number of individuals: 50 #> // Group sizes: 50 #> // Number of alleles per locus: 7 6 8 5 7 6 5 5 9 6 10 9 10 9 9 5 5 10 9 9 11 8 10 8 6 8 8 8 13 6 #> // Number of alleles per group: 235 #> // Percentage of missing data: 0.87 % #> // Observed heterozygosity: 0.66 0.66 0.76 0.76 0.69 0.58 0.64 0.7 0.75 0.8 0.76 0.82 0.73 0.7 0.7 0.78 0.66 0.8 0.8 0.66 0.9 0.41 0.79 0.84 0.72 0.62 0.6 0.64 0.84 0.42 #> // Expected heterozygosity: 0.71 0.61 0.74 0.73 0.75 0.64 0.58 0.6 0.66 0.76 0.81 0.83 0.75 0.78 0.82 0.76 0.59 0.78 0.83 0.63 0.82 0.42 0.8 0.8 0.73 0.61 0.74 0.65 0.83 0.44# \dontrun{ # Parametric Bootstrap: do not maintain allelic state or heterozygosity summary(shufflepop(Zebu, method=2))#> #> // Number of individuals: 50 #> // Group sizes: 50 #> // Number of alleles per locus: 7 6 8 5 7 6 4 5 8 6 10 9 8 9 8 5 5 8 9 9 11 6 8 8 6 8 6 7 12 5 #> // Number of alleles per group: 219 #> // Percentage of missing data: 0 % #> // Observed heterozygosity: 0.68 0.64 0.62 0.74 0.76 0.62 0.58 0.6 0.58 0.68 0.82 0.92 0.74 0.78 0.84 0.76 0.6 0.74 0.74 0.62 0.84 0.44 0.7 0.9 0.66 0.68 0.84 0.66 0.78 0.4 #> // Expected heterozygosity: 0.76 0.64 0.67 0.74 0.76 0.59 0.61 0.57 0.7 0.74 0.81 0.84 0.74 0.75 0.81 0.77 0.55 0.78 0.79 0.64 0.8 0.38 0.77 0.79 0.69 0.62 0.73 0.66 0.83 0.45# Non-Parametric Bootstrap: do not maintain allelic state or heterozygosity. summary(shufflepop(Zebu, method=3))#> #> // Number of individuals: 50 #> // Group sizes: 50 #> // Number of alleles per locus: 7 6 8 5 7 6 5 5 9 6 10 9 10 9 9 5 5 10 9 9 11 8 10 8 6 8 8 8 13 6 #> // Number of alleles per group: 235 #> // Percentage of missing data: 0 % #> // Observed heterozygosity: 0.9 0.9 0.84 0.78 0.76 0.76 0.84 0.84 0.86 0.92 0.92 0.9 0.96 0.96 0.82 0.72 0.86 0.86 0.92 0.88 0.9 0.86 0.84 0.92 0.82 0.84 0.84 0.84 0.86 0.84 #> // Expected heterozygosity: 0.86 0.83 0.86 0.8 0.85 0.82 0.79 0.79 0.88 0.82 0.89 0.88 0.89 0.88 0.88 0.79 0.8 0.89 0.88 0.88 0.9 0.87 0.89 0.87 0.82 0.87 0.86 0.87 0.9 0.82#> #> // Number of individuals: 50 #> // Group sizes: 50 #> // Number of alleles per locus: 7 6 8 5 7 6 5 5 9 6 10 9 10 9 9 5 5 10 9 9 11 8 10 8 6 8 8 8 13 6 #> // Number of alleles per group: 235 #> // Percentage of missing data: 0.87 % #> // Observed heterozygosity: 0.54 0.58 0.7 0.67 0.48 0.6 0.46 0.5 0.71 0.8 0.74 0.86 0.78 0.72 0.9 0.82 0.62 0.74 0.82 0.64 0.8 0.41 0.6 0.76 0.58 0.52 0.76 0.66 0.82 0.4 #> // Expected heterozygosity: 0.71 0.61 0.74 0.73 0.75 0.64 0.58 0.6 0.66 0.76 0.81 0.83 0.75 0.78 0.82 0.76 0.59 0.78 0.83 0.63 0.82 0.42 0.8 0.8 0.73 0.61 0.74 0.65 0.83 0.44# }