Methodology article
Using genetic markers to orient the edges in quantitative trait networks: The NEO software
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* Corresponding author: Steve Horvath shorvath@mednet.ucla.edu
1 Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
2 Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, USA
3 Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, USA
4 Biostatistics, School of Public Health, University of California, Los Angeles, USA
BMC Systems Biology 2008, 2:34 doi:10.1186/1752-0509-2-34
Published: 15 April 2008Additional files
Additional file 1:
Single edge simulation study. This document describes our single edge simulation studies involving the LEO.NB.CPA score (Eq. 5) and the LEO.NB.OCA score (Eq. 6). We describe the parameters used in the single edge A ← B simulation model. A hidden confounder C affects the correlation between A and B. The effect of SNP markers on traits A and B is parameterized with the restricted heritabilities. The single edge simulation model is used i) to study the choice of thresholds for the LEO.NB scores, ii) to compare the LEO.NB.CPA with LEO.NB.OCA scores, and iii) to evaluate automatic SNP selection methods.
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