1
|
Mandal S, Kim DH, Hua X, Li S, Shi J. Estimating the overall fraction of phenotypic variance attributed to high-dimensional predictors measured with error. Biostatistics 2024; 25:486-503. [PMID: 36797830 PMCID: PMC11017132 DOI: 10.1093/biostatistics/kxad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
In prospective genomic studies (e.g., DNA methylation, metagenomics, and transcriptomics), it is crucial to estimate the overall fraction of phenotypic variance (OFPV) attributed to the high-dimensional genomic variables, a concept similar to heritability analyses in genome-wide association studies (GWAS). Unlike genetic variants in GWAS, these genomic variables are typically measured with error due to technical limitation and temporal instability. While the existing methods developed for GWAS can be used, ignoring measurement error may severely underestimate OFPV and mislead the design of future studies. Assuming that measurement error variances are distributed similarly between causal and noncausal variables, we show that the asymptotic attenuation factor equals to the average intraclass correlation coefficients of all genomic variables, which can be estimated based on a pilot study with repeated measurements. We illustrate the method by estimating the contribution of microbiome taxa to body mass index and multiple allergy traits in the American Gut Project. Finally, we show that measurement error does not cause meaningful bias when estimating the correlation of effect sizes for two traits.
Collapse
Affiliation(s)
- Soutrik Mandal
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - Do Hyun Kim
- Department of Biostatistics, Fielding School of Public Health, University of California at Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Xing Hua
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Shilan Li
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD 20892, USA
| |
Collapse
|
2
|
Janamiri F, Rasekh A, Chaji A, Babadi B. Ridge estimation in linear mixed measurement error models using generalized maximum entropy. STATISTICS-ABINGDON 2022. [DOI: 10.1080/02331888.2022.2126474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Fariba Janamiri
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Abdolrahman Rasekh
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Alireza Chaji
- Department of Electrical Engineering, Shohadaye Hoveizeh Campus of Technology, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Babak Babadi
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| |
Collapse
|
3
|
Yavarizadeh B, Ahmed SE. The new mixed ridge estimator in a linear mixed model with measurement error under stochastic linear mixed restrictions. COMMUN STAT-SIMUL C 2021. [DOI: 10.1080/03610918.2021.1874989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
| | - Syed Ejaz Ahmed
- Department of Mathematics, Brock University, St. Catharines, Canada
| |
Collapse
|
4
|
Yavarizadeh B, Ahmed SE. The weighted ridge estimation for linear mixed models with measurement error under stochastic linear mixed restrictions. COMMUN STAT-THEOR M 2021. [DOI: 10.1080/03610926.2021.1927097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Bahareh Yavarizadeh
- Department of Mathematics and Statistics, Brock University, St.Catharines, Canada
| | - S. Ejaz Ahmed
- Department of Mathematics and Statistics, Brock University, St.Catharines, Canada
| |
Collapse
|
5
|
Maksaei N, Rasekh A, Babadi B. Influence measures and outliers detection in linear mixed measurement error models with Ridge estimation. COMMUN STAT-SIMUL C 2021. [DOI: 10.1080/03610918.2021.1926502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Najmieh Maksaei
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Abdolrahman Rasekh
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Babak Babadi
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| |
Collapse
|
6
|
Yavarizadeh B, Rasekh A, Babadi B. Estimation of parameters in linear mixed measurement error models with stochastic linear restrictions. COMMUN STAT-THEOR M 2020. [DOI: 10.1080/03610926.2019.1622730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Abdolrahman Rasekh
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Babak Babadi
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| |
Collapse
|
7
|
Emami H, Mosammam AM. Assessment of local influence in spatial elliptical linear measurement error models. COMMUN STAT-THEOR M 2020. [DOI: 10.1080/03610926.2020.1793204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Hadi Emami
- Department of Statistics, University of Zanjan, Zanjan, Iran
| | - Ali M. Mosammam
- Department of Statistics, University of Zanjan, Zanjan, Iran
| |
Collapse
|
8
|
Emami H. Improved estimation in elliptical linear mixed measurement error models. J STAT COMPUT SIM 2020. [DOI: 10.1080/00949655.2020.1743992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Hadi Emami
- Department of statistics, University of Zanjan, Zanjan, Iran
| |
Collapse
|
9
|
Yavarizadeh B, Rasekh A, Ahmed SE, Babadi B. Ridge estimation in linear mixed measurement error models with stochastic linear mixed restrictions. COMMUN STAT-SIMUL C 2019. [DOI: 10.1080/03610918.2019.1705974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Abdolrahman Rasekh
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Syed Ejaz Ahmed
- Department of Mathematics, Brock University, St.Catharines, Canada
| | - Babak Babadi
- Department of Statistics, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| |
Collapse
|
10
|
Ghapani F. Stochastic restricted Liu estimator in linear mixed measurement error models. COMMUN STAT-SIMUL C 2019. [DOI: 10.1080/03610918.2019.1664581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Fatemeh Ghapani
- Department of Mathematics and Statistics, Shoushtar Branch, Islamic Azad University, Shoushtar, Iran
| |
Collapse
|
11
|
Lac LA, Hossain S. Non-penalty shrinkage estimation of random effect models for longitudinal data with AR(1) errors. J STAT COMPUT SIM 2018. [DOI: 10.1080/00949655.2018.1511713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Le An Lac
- Department of Statistics, University of Winnipeg, Winnipeg, MB, Canada
| | - Shakhawat Hossain
- Department of Mathematics and Statistics, University of Winnipeg, Winnipeg, Canada
| |
Collapse
|
12
|
Xu L, Guo H, Yu S. Generalized p value tests for variance components in a class of linear mixed models. Stat Pap (Berl) 2018. [DOI: 10.1007/s00362-016-0778-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
13
|
Babadi B, Rasekh A, Zare K, Rasekhi AA. A variance shift model for detection of outliers in the linear mixed measurement error models. COMMUN STAT-THEOR M 2016. [DOI: 10.1080/03610926.2014.980517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
14
|
Kheradmandi A, Rasekh A. Estimation in skew-normal linear mixed measurement error models. J MULTIVARIATE ANAL 2015. [DOI: 10.1016/j.jmva.2014.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
15
|
|