An Efficient Approach to Screening Epigenome-Wide Data
Joint Authors
Karmaus, Wilfried J.
Ray, Meredith A.
Tong, Xin
Lockett, Gabrielle A.
Zhang, Hongmei
Source
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-16, 16 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-03-13
Country of Publication
Egypt
No. of Pages
16
Main Subjects
Abstract EN
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.
American Psychological Association (APA)
Ray, Meredith A.& Tong, Xin& Lockett, Gabrielle A.& Zhang, Hongmei& Karmaus, Wilfried J.. 2016. An Efficient Approach to Screening Epigenome-Wide Data. BioMed Research International،Vol. 2016, no. 2016, pp.1-16.
https://search.emarefa.net/detail/BIM-1097118
Modern Language Association (MLA)
Ray, Meredith A.…[et al.]. An Efficient Approach to Screening Epigenome-Wide Data. BioMed Research International No. 2016 (2016), pp.1-16.
https://search.emarefa.net/detail/BIM-1097118
American Medical Association (AMA)
Ray, Meredith A.& Tong, Xin& Lockett, Gabrielle A.& Zhang, Hongmei& Karmaus, Wilfried J.. An Efficient Approach to Screening Epigenome-Wide Data. BioMed Research International. 2016. Vol. 2016, no. 2016, pp.1-16.
https://search.emarefa.net/detail/BIM-1097118
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1097118