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).
ip_g(ped, d, name_to = "g", Fcol = NULL) The input dataframe, plus an additional column containing purged inbreeding coefficient values (named "g" and followed by the purging coefficient value by default).
A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.
Purging coefficient (taking values between 0.0 and 0.5).
A string naming the new output column.
Name of column with inbreeding coefficient values. If none is used, inbreeding will be computed.
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.
ip_F exp_g
data(dama)
dama <- ip_g(dama, d = 0.23)
tail(dama)
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