Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps
by Haiyong Liao, Michael Ng, Eric Fung, Pak C. Sham
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 4, No. 4, 2008

Abstract: The main aim of this paper is to propose and develop a unidimensional nonnegative scaling model to construct Linkage Disequilibrium (LD) maps. The proposed constrained scaling model can be efficiently solved by transforming it to an unconstrained model. The method is implemented in PC Clusters at Hong Kong Baptist University. The LD maps are constructed for four populations from Hapmap data sets with chromosomes of several ten thousand Single Nucleotide Polymorphisms (SNPs). The similarities and dissimilarities of the LD maps are studied and analysed. Computational results are also reported to show the effectiveness of the method using parallel computation.

Online publication date: Sat, 08-Nov-2008

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