Round Robin Multilocus Genotypes

Source: R/round_robin.R

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.

rrmlg(gid)

Arguments

gid

a genind, genclone, or loci object.

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.

See also

rraf, pgen, psex

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 
# }