rrmlg: Round Robin Multilocus Genotypes

In poppr: Genetic Analysis of Populations with Mixed Reproduction

Description

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.

Usage

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.

Author(s)

Zhian N. Kamvar, Jonah Brooks, Stacy A. Krueger-Hadfield, Erik Sotka

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)
## Not run: 
# You can find out how many unique genotypes are found without each locus:

colSums(!apply(pmlg_rr, 2, duplicated))

## End(Not run)

poppr documentation built on Sept. 7, 2021, 9:06 a.m.