This decomposition is a mathematical method for taking the square root of a symmetric matrix. The Cholesky root of a matrix A is L , where A = LL` , and L is a lower-triangular matrix. It is useful in QTL analysis because it allows modeling of a pedigree -induced covariance structure via a mixed model .Note : If this box is not checked, the original kinship or covariance matrix is included in the output data set.