A comparison of principal component methods between multiple phenotype regression and multiple SNP regression in genetic association studies

DOI10.1214/19-AOAS1312zbMATH Open1441.62171OpenAlexW3017329137MaRDI QIDQ2179976FDOQ2179976

Authors: Ian Barnett, Xihong Lin, Zhong-Hua Liu 

Publication date: 13 May 2020

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL: https://projecteuclid.org/euclid.aoas/1587002681

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zbMATH Keywords

dimension reductionhypothesis testingprincipal component analysiseigenvaluesminimum \(p\)-value testmultiple phenotypesSNP-setvariance-component test

Mathematics Subject Classification ID

Factor analysis and principal components; correspondence analysis (62H25) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to biology and medical sciences; meta analysis (62P10) Protein sequences, DNA sequences (92D20)

Cites Work

• A Geometric Perspective on the Power of Principal Component Association Tests in Multiple Phenotype Studies
• Variance component testing in generalised linear models with random effects
• Multiple phenotype association tests using summary statistics in genome-wide association studies

Cited In (10)

• Visualizing genetic constraints
• Principal component analysis (PCA) for high-dimensional data. PCA is dead. Long live PCA
• A comparison of multifactor dimensionality reduction and \(L_{1}\)-penalized regression to identify gene-gene interactions in genetic association studies
• Principal component analysis of canine hip dysplasia phenotypes and their statistical power for genome-wide association mapping
• A Geometric Perspective on the Power of Principal Component Association Tests in Multiple Phenotype Studies
• Data reduction prior to inference: are there consequences of comparing groups using a \(t\)-test based on principal component scores?
• Estimating and correcting optimism bias in multivariate PLS regression: application to the study of the association between single nucleotide polymorphisms and multivariate traits in attention deficit hyperactivity disorder
• Comparing the performance of linear and nonlinear principal components in the context of high-dimensional genomic data integration
• Genetic association test based on principal component analysis
• Analyzing multiple phenotypes based on principal component analysis

Uses Software

• PLINK
• MPAT
• Eigenstrat

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