rrmlg: Round Robin Multilocus Genotypes

In grunwaldlab/poppr: Genetic Analysis of Populations with Mixed Reproduction

Round Robin Multilocus Genotypes

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)

grunwaldlab/poppr documentation built on March 18, 2024, 11:24 p.m.