ip_Fa: Ancestral inbreeding coefficient

In purgeR: Inbreeding-Purging Estimation in Pedigreed Populations

Ancestral inbreeding coefficient

Description

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).

Usage

ip_Fa(ped, name_to = "Fa", genedrop = 0, seed = NULL, Fcol = NULL)

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.

Value

The input dataframe, plus an additional column with individual ancestral inbreeding coefficient values (named "Fa" by default).

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.

See Also

ip_F, exp_Fa

Examples

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)

purgeR documentation built on May 29, 2024, 7:24 a.m.