CRAN:https://CRAN.R-project.org/package=coxmeg
Development version: https://github.com/lhe17/coxmeg
coxmeg is an R package for efficiently conducting genome-wide association analysis (GWAS) of age-at-onset traits using a Cox mixed-effects model. Compared to coxme, coxmeg substantially improves the computational efficiency for estimating or testing genetic effects by using a variance component estimated once from a null model, and introducing fast algorithms, including inexact newton methods, preconditioned conjugate gradient methods and stochastic Lanczos quadrature. Moreover, compared to the coxme package, which is optimized only for block-diagonal matrices, coxmeg is efficient for both general sparse and dense relatedness matrices. coxmeg can also handle positive semidefinite relatedness matrices, which are common in GWAS, but not supported in coxme.
References:
- He L. and Kulminski A.M. (2019) Fast Algorithms for Conducting Large-Scale GWAS of Age-at-Onset Traits Using Cox Mixed-Effects Models. [ doi:10.1534/genetics.119.302940 ] [ PMID: 32132097 ] [ PMCID: PMC7404243 ]
