ip_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

ip_g(ped, d, name_to = "g<d>", Fcol = NULL)

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).
name_to	A string naming the new output column.
Fcol	Name of column with inbreeding coefficient values. If none is used, inbreeding will be computed.

Value

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

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.

See Also

ip_F exp_g

Examples

data(dama)
dama <- ip_g(dama, d = 0.23)
tail(dama)

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