Calculating and Inferring Relatedness Coefficients with BGmisc
Source:vignettes/analyticrelatedness.Rmd
analyticrelatedness.Rmd
Introduction
This vignette focuses on the calculation and inference of relatedness
coefficients using the BGmisc
package. The relatedness
coefficient is a measure of the genetic relationship between two
individuals. Here, we introduce two functions:
calculateRelatedness
and inferRelatedness
,
which allow users to compute and infer the relatedness coefficient
respectively.
Calculating Relatedness Coefficient
The calculateRelatedness
function offers a method to
compute the relatedness coefficient based on shared ancestry, as
described by Wright (1922). This function utilizes the formula:
\[ r_{bc} = \sum \left(\frac{1}{2}\right)^{n+n'+1} (1+f_a) \]
Where \(n\) and \(n'\) represent the number of generations back of common ancestors the pair share.
# Example usage:
# For full siblings, the relatedness coefficient is expected to be 0.5:
calculateRelatedness(generations = 1, full = TRUE)
#> [1] 0.5
# For half siblings, the relatedness coefficient is expected to be 0.25:
calculateRelatedness(generations = 1, full = FALSE)
#> [1] 0.25
Inferring Relatedness Coefficient
The inferRelatedness
function is designed to infer the
relatedness coefficient between two groups based on the observed
correlation between their additive genetic variance and shared
environmental variance. This function leverages the ACE framework.
# Example usage:
# Infer the relatedness coefficient:
inferRelatedness(obsR = 0.5, aceA = 0.9, aceC = 0, sharedC = 0)
#> [1] 0.5555556