Model-Free Analysis and Permutation Tests for Allelic AssociationsZhao J.H.a · Curtis D.b · Sham P.C.a
aDepartment of Psychological Medicine, Institute of Psychiatry, and bJoint Academic Department of Psychological Medicine, St. Bartholomew’s and Royal London School of Medicine and Dentistry, London, UK
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In this short report, we address some practical problems in performing likelihood-based allelic association analysis of case-control data. Model-free statistics are proposed and their properties assessed by simulation, and procedures based on permutation tests are described for marker-marker as well as marker-disease associations. A memory-efficient algorithm is developed which enables several highly polymorphic markers to be analysed.
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