Fis: Fis

In dbailleul/RClone: Partially Clonal Populations Analysis

Description

Fis computes observed Heterozygosity (Hobs), expected Heterozygosity (Hexp; Nei, 1978) and Fis from ramets or genets.

Usage

Fis(data1, vecpop, genet = FALSE, RR = FALSE)

Arguments

data1	a Rclone table with one allele per column for diploid data.
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, Fis and allelic frequencies are computed with Round-Robin method.

Details

Allelic frequencies are computed:

• on ramet level,

• on genet level (genet = TRUE),

• with Round-Robin method (RR = TRUE, see freq_RR).

Value

a table with Hobs, Hexp and Fis for each locus.

If RR = TRUE, a list of the Hobs/Hexp/Fis table and another table with Round-Robin frequencies.

If data1 is a multi-population table, a list of table(s) for each population.

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, pgen, pgen_Fis, psex and psex_Fis

Examples

data(posidonia)

Fis(posidonia)
Fis(posidonia, genet = TRUE)
Fis(posidonia, RR = TRUE)

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