Fa: Ancestral inbreeding coefficient
In purgeR: Inbreeding-Purging Estimation in Pedigreed Populations
Fa R Documentation
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
Fa(ped, Fi, name_to, genedrop = 0L, seed = NULL)
Arguments
ped
A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns.
Fi
Vector of inbreeding coefficient values
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.
Value
The input dataframe, plus an additional column named "Fa" with individual ancestral inbreeding coefficient values.
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.
purgeR documentation built on Aug. 16, 2023, 9:07 a.m.
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| Fa | R Documentation |
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
Fa(ped, Fi, name_to, genedrop = 0L, seed = NULL)
Arguments
ped |
A dataframe containing the pedigree. Individual (id), maternal (dam), and paternal (sire) identities are mandatory columns. |
Fi |
Vector of inbreeding coefficient values |
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. |
Value
The input dataframe, plus an additional column named "Fa" with individual ancestral inbreeding coefficient values.
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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