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purgeR (version 1.8.2)

ip_Fa: 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)

Value

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.

See Also

ip_F, exp_Fa

Examples

Run this code
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)

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