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A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

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Published on: July 1, 2020

Empirical pathway analysis, without permutation.

Yi-Hui Zhou1, William T Barry, Fred A Wright

  • 1Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA. yihuiz@live.unc.edu

Biostatistics (Oxford, England)
|February 23, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces analytic approximations for permutation pathway analysis, significantly reducing computational demands. These methods maintain accuracy, offering a faster alternative for gene expression analysis.

Keywords:
Gene setsMultiple hypothesis testingPermutation approximation

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Statistical Genetics

Background:

  • Resampling-based expression pathway analysis controls type I error rates, unlike simple gene-list methods.
  • Resampling methods are computationally intensive, requiring significant time and memory.

Purpose of the Study:

  • To develop accurate analytic approximations for permutation pathway analysis.
  • To reduce the computational burden of pathway analysis while preserving statistical rigor.

Main Methods:

  • Developed novel analytic approximations for score statistics, including Pearson's correlation and summed scores.
  • Implemented and tested procedures using simulations based on real datasets.
  • Extended methods to incorporate covariates and censored data.

Main Results:

  • Analytic approximations demonstrate good performance, even with small sample sizes.
  • The proposed methods significantly reduce computation time and memory requirements.
  • The R package safeExpress implements these efficient approaches.

Conclusions:

  • Analytic approximations offer a computationally efficient alternative to resampling for pathway analysis.
  • These methods retain the statistical advantages of permutation testing.
  • The safeExpress R package facilitates the application of these advanced techniques.