Technical note: Determining peeling order using sparse matrix algorithms

Abstract

To study the effect of individual genes by segregation or linkage analyses, the likelihood of the model needs to be evaluated. The likelihood can be computed efficiently using the Elston-Stewart algorithm. This algorithm involves summing over the unobserved genotypes in the pedigree, which is called peeling. An important aspect of this algorithm is to determine the order of peeling to maximize efficiency. This paper shows how determining peeling order is related to a problem in solving systems of symmetric sparse linear equations. It also shows how algorithms developed to efficiently solve those systems, can be used to determine the optimal order of peeling in the Elston-Stewart algorithm.