The vcpen Package

Penalized Variance Component analysis is performed by the vcpen function. The calculations do..Dan please edit…

The vcpen() Function

vcpen() is a function that performs penalized model fitting of variance components. The variance components are pre-calculated matrices of similarity between subjects, including residual error matrix.

The kernel_linear() Function

kernel_linear() calculates a kernel matrix of genomic similarity from SNP dosage, where the rows are subjects, and columns are the minor allele dosage (0/1/2), assuming bi-allelic SNPs.