Round Robin Allele Frequencies
This function utilizes
rrmlg to calculate multilocus genotypes
and then subsets each locus by the resulting MLGs to calculate the
round-robin allele frequencies used for pgen and psex.
a genind or genclone object
either a formula to set the population factor from the
either "list" (default), "vector", or "data.frame".
When this is
a logical indicating whether or not zero-valued allele
frequencies should be corrected using the methods outlined in
correcting rare alleles.
options from correcting rare alleles. The default is to correct allele frequencies to 1/n
Calculating allele frequencies for clonal populations is a difficult task. Frequencies calculated on non-clone-corrected data suffer from bias due to non-independent samples. On the other hand, frequencies calculated on clone-corrected data artificially increases the significance of rare alleles. The method of round-robin allele frequencies as presented in Parks and Werth (1993) provides a method of calculating allele frequencies in a way that minimizes both of these effects.
Allele frequencies at a given locus are
calculated based on samples that are clone corrected without that
locus. When this happens, rare alleles have a high likelihood of dropping
out, giving them a frequency of "0". For some analyses, this is a perfectly
fine outcome, but for analyses such as
psex, this could result in undefined values. Setting
correction = TRUE will allow you to control how these zero-valued
allele frequencies are corrected. For details, please see the documentation
on correcting rare alleles and examples.
a vector or list of allele frequencies
by_pop = TRUE, the output will be a matrix of allele
frequencies. Additionally, when the argument
pop is not
by_pop is automatically
Zhian N. Kamvar, Jonah Brooks, Stacy A. Krueger-Hadfield, Erik Sotka
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.
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data(Pram) # Round robin allele frequencies, correcting zero-valued frequencies to 1/nInd(Pram) rraf(Pram) ## Not run: ## Round robin allele frequencies will be different than observed # Compare to without round robin: PrLoc <- seploc(Pram, res = "mat") # get locus by matrix lapply(PrLoc, colMeans, na.rm = TRUE) # Without round robin, clone corrected: Pcc <- clonecorrect(Pram, strata = NA) # indiscriminantly clone correct PccLoc <- seploc(Pcc, res = "mat") lapply(PccLoc, colMeans, na.rm = TRUE) ## Different methods of obtaining round robin allele frequencies # Get vector output. rraf(Pram, res = "vector") # Getting the output as a data frame allows us to use ggplot2 to visualize (Prdf <- rraf(Pram, res = "data.frame")) library("ggplot2") ggplot(Prdf, aes(y = allele, x = frequency)) + geom_point() + facet_grid(locus ~ ., scale = "free_y", space = "free") ## Round Robin allele frequencies by population (matrix only) # By default, allele frequencies will be corrected by 1/n per population (Prbp <- rraf(Pram, by_pop = TRUE)) # This might be problematic because populations like PistolRSF_OR has a # population size of four. # By using the 'e' argument to rare_allele_correction, this can be set to a # more reasonable value. (Prbp <- rraf(Pram, by_pop = TRUE, e = 1/nInd(Pram))) ## End(Not run)