Computes the ancestral inbreeding coefficient (Fa).
This is the probability that an allele has been in homozygosity in at least one ancestor (Ballou 1997).
A genedrop approach is included to compute unbiased estimates of Fa (Baumung et al. 2015).
The input dataframe, plus an additional column with individual ancestral inbreeding coefficient values (named "Fa" by default).
Arguments
ped
A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.
name_to
A string naming the new output column.
genedrop
Number of genedrop iterations to run. If set to zero (as default), Ballou's Fa is computed.
seed
Sets a seed for the random number generator.
Fcol
Name of column with inbreeding coefficient values. If none is used, inbreeding will be computed.
References
Ballou JD. 1997. Ancestral inbreeding only minimally affects inbreeding depression in mammalian populations. J Hered. 88:169–178.
Baumung et al. 2015. GRAIN: A computer program to calculate ancestral and partial inbreeding coefficients using a gene dropping approach. Journal of Animal Breeding and Genetics 132: 100-108.
data(dama)
# dama <- ip_Fa(dama) # Compute F on the go (won't be kept in the pedigree).dama <- ip_F(dama)
dama <- ip_Fa(dama, Fcol = 'Fi') # If F is computed in advance.tail(dama)