r2VIM: A new variable selection method for random forests in genome-wide association studies

BioData Mining
Silke SzymczakJoan E Bailey-Wilson

Abstract

Machine learning methods and in particular random forests (RFs) are a promising alternative to standard single SNP analyses in genome-wide association studies (GWAS). RFs provide variable importance measures (VIMs) to rank SNPs according to their predictive power. However, in contrast to the established genome-wide significance threshold, no clear criteria exist to determine how many SNPs should be selected for downstream analyses. We propose a new variable selection approach, recurrent relative variable importance measure (r2VIM). Importance values are calculated relative to an observed minimal importance score for several runs of RF and only SNPs with large relative VIMs in all of the runs are selected as important. Evaluations on simulated GWAS data show that the new method controls the number of false-positives under the null hypothesis. Under a simple alternative hypothesis with several independent main effects it is only slightly less powerful than logistic regression. In an experimental GWAS data set, the same strong signal is identified while the approach selects none of the SNPs in an underpowered GWAS. The novel variable selection method r2VIM is a promising extension to standard RF for objectively selecting relevant ...Continue Reading

References

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Citations

Mar 24, 2017·BioData Mining·Nestor Rodriguez, Sergio Rojas-Galeano
Mar 6, 2018·Molecular Ecology Resources·Marine S O BrieucKerry A Naish
May 15, 2018·Bioinformatics·Stefano NembriniMarvin N Wright
Jun 22, 2018·PloS One·Alexander KirpichLauren M McIntyre
Jan 25, 2019·PloS One·Shuzhen SunCharles Chen
Oct 19, 2017·Briefings in Bioinformatics·Frauke DegenhardtSilke Szymczak
Oct 10, 2019·Bioinformatics·Andrew W GeorgeJoshua Bowden
Oct 31, 2020·Briefings in Bioinformatics·Shanwen SunQuan Zou
Nov 12, 2020·Journal of Personalized Medicine·Solomon M AdamsArthur F Harralson
Oct 23, 2020·Genome Génome / Conseil National De Recherches Canada·Sarah J MacEachern, Nils D Forkert

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Methods Mentioned

BETA
chip

Software Mentioned

GWAsimulator
r2VIM
cforest
R
SeqSIMLA2
PLINK
RandomJungle
GUIDE
Biowulf Linux

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