This function will mask each locus one by one and then calculate multilocus genotypes from the remaining loci in a round-robin fashion. This is used for calculating the round robin allele frequencies for pgen and psex.
Value
a matrix of multilocus genotype assignments by masked locus. There will be n rows and m columns where n = number of samples and m = number of loci.
References
Arnaud-Haond, S., Duarte, C. M., Alberto, F., & Serrão, E. A. 2007. Standardizing methods to address clonality in population studies. Molecular Ecology, 16(24), 5115-5139.
Parks, J. C., & Werth, C. R. 1993. A study of spatial features of clones in a population of bracken fern, Pteridium aquilinum (Dennstaedtiaceae). American Journal of Botany, 537-544.
Examples
# Find out the round-robin multilocus genotype assignments for P. ramorum
data(Pram)
pmlg_rr <- rrmlg(Pram)
head(pmlg_rr)
#> PrMS6A1 Pr9C3A1 PrMS39A1 PrMS45A1 PrMS43A1
#> [1,] 61 61 35 52 9
#> [2,] 28 28 44 26 7
#> [3,] 75 75 51 67 9
#> [4,] 16 16 22 14 7
#> [5,] 27 27 43 25 7
#> [6,] 28 28 44 26 7
# \dontrun{
# You can find out how many unique genotypes are found without each locus:
colSums(!apply(pmlg_rr, 2, duplicated))
#> PrMS6A1 Pr9C3A1 PrMS39A1 PrMS45A1 PrMS43A1
#> 97 98 66 87 13
# }