geneJAM-package: geneJAM:

geneJAM-packageR Documentation

geneJAM:

Description

A package implementing methods for clustering traits that share some genetic component via polygenic scores (PSs). It fits a sparse precision matrix of the PSs via graphical lasso. The regularisation path is computed for the lasso penalty rho at a grid of values for the regularisation parameter rho. A cross-validation method for tuning the penalty rho is provided.

Details

The geneJAM package provides three categories of important functions: simple fit, cross-validation and plots.

fit

The function geneJAM clusters outcome components (traits) that share some feature (genetic component) via polygenic scores (PSs). It fits a sparse precision matrix via graphical lasso. The regularisation path is computed for the lasso penalty at a grid of values for the regularisation parameter rho. The clusters are used to specify the structure of the error covariance matrix of a GLS model and the feasible GLS estimator is used for estimating the unknown parameters in a linear regression model with a certain unknown degree of correlation between the residuals.

Author(s)

Ann-Sophie Buchardt asbu@sund.ku.dk
Maintainer: Ann-Sophie Buchardt asbu@sund.ku.dk

References

glasso, glmnet


abuchardt/EdGwas documentation built on Nov. 28, 2022, 11:49 a.m.