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Abstract Adaptive multiple testing with covariates is an important research direction that has gained major attention in recent years. It has been widely recognised that leveraging side information provided by auxiliary covariates can improve the power of false discovery rate (FDR) procedures. Currently, most such procedures are devised with p-values as their main statistics. However, for two-sided hypotheses, the usual data processing step that transforms the primary statistics, known as p-values, into p-values not only leads to a loss of information carried by the main statistics, but can also undermine the ability of the covariates to assist with the FDR inference. We develop a p-value based covariate-adaptive (ZAP) methodology that operates on the intact structural information encoded jointly by the p-values and covariates. It seeks to emulate the oracle p-value procedure via a working model, and its rejection regions significantly depart from those of the p-value adaptive testing approaches. The key strength of ZAP is that the FDR control is guaranteed with minimal assumptions, even when the working model is misspecified. We demonstrate the state-of-the-art performance of ZAP using both simulated and real data, which shows that the efficiency gain can be substantial in comparison with p-value-based methods. Our methodology is implemented in the R package zap.
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Catch me if you can: signal localization with knockoff e -values
Abstract We consider problems where many, somewhat redundant, hypotheses are tested and we are interested in reporting the most precise rejections, with false discovery rate (FDR) control. This is the case, for example, when researchers are interested both in individual hypotheses as well as group hypotheses corresponding to intersections of sets of the original hypotheses, at several resolution levels. A concrete application is in genome-wide association studies, where, depending on the signal strengths, it might be possible to resolve the influence of individual genetic variants on a phenotype with greater or lower precision. To adapt to the unknown signal strength, analyses are conducted at multiple resolutions and researchers are most interested in the more precise discoveries. Assuring FDR control on the reported findings with these adaptive searches is, however, often impossible. To design a multiple comparison procedure that allows for an adaptive choice of resolution with FDR control, we leverage e-values and linear programming. We adapt this approach to problems where knockoffs and group knockoffs have been successfully applied to test conditional independence hypotheses. We demonstrate its efficacy by analysing data from the UK Biobank.
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- Award ID(s):
- 2210392
- PAR ID:
- 10512708
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- Journal of the Royal Statistical Society Series B: Statistical Methodology
- Volume:
- 87
- Issue:
- 1
- ISSN:
- 1369-7412
- Format(s):
- Medium: X Size: p. 56-73
- Size(s):
- p. 56-73
- Sponsoring Org:
- National Science Foundation
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