Maximal conditional chi-square importance in random forests.

Bioinformatics
Minghui WangHeping Zhang

Abstract

High-dimensional data are frequently generated in genome-wide association studies (GWAS) and other studies. It is important to identify features such as single nucleotide polymorphisms (SNPs) in GWAS that are associated with a disease. Random forests represent a very useful approach for this purpose, using a variable importance score. This importance score has several shortcomings. We propose an alternative importance measure to overcome those shortcomings. We characterized the effect of multiple SNPs under various models using our proposed importance measure in random forests, which uses maximal conditional chi-square (MCC) as a measure of association between a SNP and the trait conditional on other SNPs. Based on this importance measure, we employed a permutation test to estimate empirical P-values of SNPs. Our method was compared to a univariate test and the permutation test using the Gini and permutation importance. In simulation, the proposed method performed consistently superior to the other methods in identifying of risk SNPs. In a GWAS of age-related macular degeneration, the proposed method confirmed two significant SNPs (at the genome-wide adjusted level of 0.05). Further analysis showed that these two SNPs conformed...Continue Reading

References

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Mar 19, 2003·Proceedings of the National Academy of Sciences of the United States of America·Heping ZhangBurton Singer
Dec 14, 2004·BMC Genetics·Kathryn L LunettaPaul Van Eerdewegh
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Jul 20, 2007·The New England Journal of Medicine·Nilesh J SamaniUNKNOWN WTCCC and the Cardiogenics Consortium
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Xiang ChenHeping Zhang
Apr 16, 2008·BMC Genomics·Chaitanya R SannaLiqing Zhang
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Oct 15, 2008·Statistics and Its Interface·Heping Zhang, Yuanqing Ye
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Citations

Jul 13, 2012·Briefings in Bioinformatics·Wouter G TouwSacha A F T van Hijum
Sep 22, 2011·Human Heredity·Annette M MolinaroNilanjan Chatterjee
Sep 14, 2012·BMC Genomics·Chrysanthi AinaliSophia Tsoka
Jan 1, 2011·Wiley Interdisciplinary Reviews. Data Mining and Knowledge Discovery·Xiang ChenHeping Zhang
Nov 5, 2014·Statistics in Medicine·Jaime Lynn SpeiserWilliam M Lee
Sep 19, 2012·IEEE Transactions on Nanobioscience·Qingyao WuMichael K Ng
May 2, 2012·Genomics·Xi Chen, Hemant Ishwaran
Jul 22, 2020·BMC Medical Informatics and Decision Making·Yueyang ZhaoSong Bai
Mar 12, 2021·G3 : Genes - Genomes - Genetics·Osval Antonio Montesinos-LópezFelícitas Alejandra Valladares-Anguiano

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