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Numericware N: Numerator Relationship Matrix Calculator
Bongsong Kim1, William D Beavis2, Jens Léon2
1From the Department of Agronomy, Iowa State University, Ames, IA 50011 (Kim and Beavis); and INRES-Plant Breeding, University of Bonn, Katzenburgweg 5, 53115 Bonn, Germany (Léon). bkim@noble.org.
Abstract:
We present the generalized numerator relationship matrix (GNRM) algorithm and Numericware N as a software tool for calculating the numerator relationship matrix (NRM). The GNRM algorithm aims to build the NRM based on plant pedigrees. Customary plant pedigrees have a sparse format representing multiple ancestors and offspring. Applying the existing NRM algorithm to plant pedigrees requires transforming the pedigree statements from sparse (multi-founders to offspring) to dense (bi-parents to offspring). The GNRM algorithm enables the computation of the NRM using sparse pedigrees. Because sparse pedigrees can be used, Numericware N produces smaller dimensions of the NRM, thus making computing time much faster. Moreover, Numericware N enables expansion of identical by state (IBS) matrix for scheduled pedigrees, which allows prediction of IBS matrix.
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