Unidimensional nonnegative scaling for genome-wide linkage disequilibrium maps.
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.
Liao
Haiyong
H
Centre for Mathematical Imaging and Vision, and Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
Ng
Michael
M
Fung
Eric
E
Sham
Pak C
PC
D002874:Chromosome Mapping / Q000706:statistics & numerical data*; D019295:Computational Biology; D030541:Databases, Genetic; D023281:Genomics / Q000706:statistics & numerical data; D006801:Humans; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D012984:Software