A simulation study to assess a variable selection method for selecting single nucleotide polymorphisms associated with disease.
Huwaida Rabie,Ian W. Saunders +1 more
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TL;DR: Simulation results showed that GeneRaVE performed well and outperformed single SNP analysis using the chi-squared method in identifying disease-related SNPs.
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Abstract: In genome-wide association studies, where hundreds of thousands of single nucleotide polymorphisms (SNPs) are genotyped, the potential for false positives is high and methods for selecting models with only a few SNPs are required. Methods for variable selection giving sets of SNPs associated with disease have been developed, but are still less common than evaluation of individual SNPs one at a time. To assess the potential improvement available from multi-SNP approaches, we examined the performance of the software GeneRaVE as a variable selection method when applied to SNP data in case-control studies. The method was assessed via simulations, in which a haplotype identified by three SNPs was taken to be associated with the disease. Simulated data sets reflecting different levels and patterns of genetic association with the disease were generated. In order to have a baseline level of performance to assess the method against, we used a generalized linear model using only the three disease susceptib...
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FARMS: A New Algorithm for Variable Selection
TL;DR: A new method to handle such complex datasets, referred to as FARMS, that combines forward and all subsets regression for model selection and is implemented in R statistical language is described, providing a new tool for the thorough analysis of complex datasets without the need for massive computational infrastructure.
References
•Journal Article
R: A language and environment for statistical computing.
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
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