| ip_g {purgeR} | R Documentation |
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
Examples
data(dama)
dama <- ip_g(dama, d = 0.23)
tail(dama)