Computes the generalized heritability of a random-effect term from a fitted linear mixed model. By default, a single scalar heritability value is returned. Optionally, a spectral decomposition is provided that reveals how genetic signal is distributed across estimable genetic directions.
Usage
getHeritability(obj, geno.term, type = c("scalar", "spectral"), tol = 1e-08)Arguments
- obj
An object of class
"LMMsolve".- geno.term
A character string giving the name of the genetic random-effect term.
- type
Character string specifying the output:
"scalar"(default) returns a single numeric heritability value;"spectral"returns a data frame with the spectral decomposition.- tol
Numerical tolerance used to determine the estimable genetic space.
Value
If type = "scalar", a numeric value giving the generalized heritability.
If type = "spectral", a data frame with columns:
- component
Index of the spectral component
- lambda
Canonical heritability for the component
- w
Weight of the component (genetic capacity)
- h2_comp
Contribution of the component to total heritability
In the spectral case, the scalar generalized heritability is also available as
the attribute "h2_G".
Details
Generalized heritability is defined as the proportion of estimable genetic signal retained by the design relative to the available genetic capacity, accounting for the genetic covariance structure.
For independent genotypes, this definition reduces to classical generalized heritability measures based on effective dimension (Cullis, Oakey, Rodríguez-Álvarez). When genotypes are correlated, the spectral decomposition reveals anisotropy in information retention across genetic directions.