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2016 ; 2016
(ä): 2615348
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An Efficient Approach to Screening Epigenome-Wide Data
#MMPMID27034928
Ray MA
; Tong X
; Lockett GA
; Zhang H
; Karmaus WJ
Biomed Res Int
2016[]; 2016
(ä): 2615348
PMID27034928
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Screening cytosine-phosphate-guanine dinucleotide (CpG) DNA methylation sites in
association with some covariate(s) is desired due to high dimensionality. We
incorporate surrogate variable analyses (SVAs) into (ordinary or robust) linear
regressions and utilize training and testing samples for nested validation to
screen CpG sites. SVA is to account for variations in the methylation not
explained by the specified covariate(s) and adjust for confounding effects. To
make it easier to users, this screening method is built into a user-friendly R
package, ttScreening, with efficient algorithms implemented. Various simulations
were implemented to examine the robustness and sensitivity of the method compared
to the classical approaches controlling for multiple testing: the false discovery
rates-based (FDR-based) and the Bonferroni-based methods. The proposed approach
in general performs better and has the potential to control both types I and II
errors. We applied ttScreening to 383,998 CpG sites in association with maternal
smoking, one of the leading factors for cancer risk.
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