g: Purged inbreeding coefficient

In purgeR: Inbreeding-Purging Estimation in Pedigreed Populations

Purged inbreeding coefficient

Description

Computes the purged inbreeding coefficient (g). This is the probability that two alleles on a locus are identical by descent, but relative to deleterious recessive alleles (García-Dorado 2012). The reduction in g relative to standard inbreeding (F) is given by an effective purging coefficient (d), that measures the strength of the deleterious recessive component in the genome. The coefficient g is computed following the methods for pedigrees in García-Dorado (2012) and García-Dorado et al. (2016).

Usage

g(ped, d, Fi, name_to)

Arguments

ped	A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.
d	Purging coefficient (taking values between 0.0 and 0.5).
Fi	Vector of inbreeding coefficient values
name_to	A string naming the new output column.

Value

The input dataframe, plus an additional column named "g" followed by the purging coefficient, containing purged inbreeding coefficient values.

References

• García-Dorado. 2012. Understanding and predicting the fitness decline of shrunk populations: Inbreeding, purging, mutation, and standard selection. Genetics 190: 1-16.

• García-Dorado et al. 2016. Predictive model and software for inbreeding-purging analysis of pedigreed populations. G3 6: 3593-3601.

purgeR documentation built on Aug. 16, 2023, 9:07 a.m.