poppr (version 2.1.0)

rraf: Round Robin Allele Frequencies

Description

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.

Usage

rraf(gid, pop = NULL, res = "list", by_pop = FALSE, correction = TRUE)

Arguments

gid

a genind or genclone object

pop

either a formula to set the population factor from the strata slot or a vector specifying the population factor for each sample. Defaults to NULL.

res

Either "list" (default), "vector", or "data.frame".

by_pop

When this is TRUE, the calculation will be done by population. Defaults to FALSE

correction

a logical indicating whether or not zero value allele frequencies should be set to 1/n (Default: TRUE)

Value

• a vector or list of allele frequencies

Details

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. This means that rare alleles might not be represented, giving them an allele frequency of "0". For some analyses, this value is perfectly fine, but for analyses such as pgen and psex, this could result in genotype probabilities of "0". One remedy for this is in the correction option. This will replace any zero-frequency alleles by 1/n, but it will mean that the sum of allele frequencies at that locus will no longer be 1.

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

rrmlg, pgen, psex

Examples

data(Pram)
# Round robin allele frequencies.
rraf(Pram)


## 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")

# Get data frame output and plot.
(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 populations (matrix only)

# Get frequencies per population without correction for zero-frequency alleles
(Prbp <- rraf(Pram, by_pop = TRUE, correction = FALSE))
# You can set the zero-frequency alleles to be 1/nInd(Pram)
Prbp[Prbp == 0] <- 1/nInd(Pram)
Prbp

# Get frequencies per population, but set zero-frequency alleles to 1/n
(Prbp <- rraf(Pram, by_pop = TRUE, correction = TRUE))