freq_RR: Allelic Frequencies

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/RClone.R

Description

freq_RR returns a table of allelic frequencies computed with or without Round-Robin method.

Usage

1
freq_RR(data1, haploid = FALSE, vecpop = NULL, genet = FALSE, RR = FALSE)

Arguments

data1

a Rclone table with one allele per column.

haploid

logical, option,haploid indicates the ploidy level of data1.

vecpop

vector, option, vecpop indicates the population name of each unit of data1, if data1 contains several populations. If data1 contains only one population, leave vecpop = NULL.

genet

option, if TRUE, data1 is reduced to genets.

RR

option, if TRUE, indicates frequencies are computed with Round-Robin method.

Details

Round-Robin method (Parks & Werth 1993) is a sub-sampling approach which avoids overestimation of rare alleles.
Each locus frequency is estimated on MLG lists constructed without the locus sampled.
This calculation is repeated for all loci.

Value

a table (one population) or a list of tables (several populations) with three columns:

Author(s)

Creator/Author: Diane Bailleul <[email protected]>
Author: Sophie Arnaud-Haond <[email protected]>
Contributor: Solenn Stoeckel

The R implementation of RClone was written by Diane Bailleul.

The design was inspired by GenClone program described in Arnaud-Haond & Belkhir (2007).

References

Parks & Werth, 1993, A study of spatial features of clones in a population of Bracken fern, Pteridium aquilinum (Dennstaedtiaceae). Arnaud-Haond et al., 2007, Standardizing methods to address clonality in population studies.

See Also

pgen and pgen_Fis

Examples

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dbailleul/RClone documentation built on May 12, 2017, 8:56 p.m.