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      A simple new approach to variable selection in regression, with application to genetic fine mapping

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          Regression Shrinkage and Selection Via the Lasso

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            Regularization and variable selection via the elastic net

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              GCTA: a tool for genome-wide complex trait analysis.

              For most human complex diseases and traits, SNPs identified by genome-wide association studies (GWAS) explain only a small fraction of the heritability. Here we report a user-friendly software tool called genome-wide complex trait analysis (GCTA), which was developed based on a method we recently developed to address the "missing heritability" problem. GCTA estimates the variance explained by all the SNPs on a chromosome or on the whole genome for a complex trait rather than testing the association of any particular SNP to the trait. We introduce GCTA's five main functions: data management, estimation of the genetic relationships from SNPs, mixed linear model analysis of variance explained by the SNPs, estimation of the linkage disequilibrium structure, and GWAS simulation. We focus on the function of estimating the variance explained by all the SNPs on the X chromosome and testing the hypotheses of dosage compensation. The GCTA software is a versatile tool to estimate and partition complex trait variation with large GWAS data sets.
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                Author and article information

                Journal
                Journal of the Royal Statistical Society: Series B (Statistical Methodology)
                J. R. Stat. Soc. B
                Wiley
                1369-7412
                1467-9868
                December 2020
                July 10 2020
                December 2020
                : 82
                : 5
                : 1273-1300
                Affiliations
                [1 ]University of Chicago USA
                Article
                10.1111/rssb.12388
                37220626
                89762e63-84f5-46fc-9fbd-cb3e5d32e108
                © 2020

                http://creativecommons.org/licenses/by/4.0/

                http://doi.wiley.com/10.1002/tdm_license_1.1

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