get_eigentraits: Calculate eigentraits
In cape: Combined Analysis of Pleiotropy and Epistasis for Diversity Outbred Mice

get_eigentraits

R Documentation

Calculate eigentraits

Description

This function uses singular value decomposition (SVD) to calculate eigentraits from the phenotype matrix in the cape data object. It adds the eigentrait matrix to the data object along with the singular values and the right singular vectors.

Usage

get_eigentraits(data_obj, scale_pheno = TRUE, normalize_pheno = TRUE)

Arguments

`data_obj`	a `Cape` object
`scale_pheno`	A logical value indicating whether to mean-center and standardize the traits.
`normalize_pheno`	A logical value indicating whether to rankZ normalize the phenotypes.

Details

If scale_pheno is TRUE, the phenotypes are mean-centered and standardized before running the svd.

Because we use SVD in this step, there can be no missing values in the phenotype matrix. Any individuals with missing values are removed with a message.