pgen: Probability of a Genotype

In dbailleul/RClone: Partially Clonal Populations Analysis

Description

pgen and pgen_Fis compute the probability of a genotype under the Hardy-Weinberg equilibrium assumption (with or without taking account of departures from H-W equilibrium).

Usage

pgen(data1, haploid = FALSE, vecpop = NULL, genet = FALSE, RR = FALSE)
pgen_Fis(data1, 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. Not edible for pgen_Fis.
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 genet = TRUE, computes pgen on genet level.
RR	option, if RR = TRUE, computes pgen with Round-Robin method.

Value

a table (one population) or a list of tables (several populations) with pgen computed for each genotype.

Note

We strongly recommand to use RR = TRUE option to compute allelic frequencies for clonal data. Otherwise, we let the options to work with frequencies at genet level (genet = TRUE) or ramet level (RR = FALSE and genet = FALSE).

Author(s)

Creator/Author: Diane Bailleul <[e-mail]>
Author: Sophie Arnaud-Haond <[e-mail]>
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

Arnaud-Haond et al., 2007, Standardizing methods to address clonality in population studies.

See Also

freq_RR, psex and psex_Fis

Examples

data(posidonia)

pgen(posidonia, RR = TRUE)
pgen_Fis(posidonia, RR = TRUE)

dbailleul/RClone documentation built on May 17, 2021, 3:04 p.m.