Correction for population stratification in random forest analysis.

ABSTRACT:

Background

Population structure (PS), including population stratification and admixture, is a significant confounder in genome-wide association studies (GWAS), as it may produce spurious associations. Random forest (RF) has been increasingly applied in GWAS data analysis because of its advantage in analysing high dimensional genetic data. RF creates importance measures for single nucleotide polymorphisms (SNPs), which are helpful for feature selections. However, if PS is not appropriately corrected, RF tends to give high importance to disease-unrelated SNPs with different frequencies of allele or genotype among subpopulations, leading to inaccurate results.

Methods

In this study, the authors propose to correct for the confounding effect of PS by including the information of

SUBMITTER: Zhao Y 

PROVIDER: S-EPMC3535752 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature