Genome-wide association analysis by lasso penalized logistic regression
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13,656 citations
Cites background from "Genome-wide association analysis by..."
...Several other researchers have also re-discovered coordinate descent, many for solving the same problems we address in this paper—notably Shevade and Keerthi (2003), Krishnapuram and Hartemink (2005), Genkin et al. (2007) and Wu et al. (2009)....
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...Several other researchers have also re-discovered coordinate descent, many for solving the same problems we address in this paper|notably Shevade and Keerthi (2003), Krishnapuram and Hartemink (2005), Genkin et al. (2007) and Wu et al. (2009) ....
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2,275 citations
1,393 citations
Cites background from "Genome-wide association analysis by..."
...The normal distribution simplifies some calculations, but various heavy-tailed distributions have also been proposed for GWAS data [38,39] and would lead to improved prediction if such models held in truth....
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796 citations
Cites methods from "Genome-wide association analysis by..."
...In fact, hierarchical models using LASSO have been successfully applied in simultaneous multivariate analyses of all GWA study SNP...
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764 citations
References
83,420 citations
"Genome-wide association analysis by..." refers background or methods in this paper
...In the Simes procedure highlighted by Benjamini and Hochberg (1995) in their analysis of FDR, there are n null hypotheses H1,....
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...In the Simes procedure highlighted by Benjamini and Hochberg (1995) in their analysis of FDR, there are n null hypotheses H1,...,Hn and n corresponding P-values P1,...,Pn. The latter are replaced by their order statistics P(1),...,P(n). If for a given α≥0, we choose the largest integer j such that P(i) ≤ (i/n)α for all i≤ j, then we can reject the hypotheses H(1), ...,H(j) at an FDR of α or better. This procedure is justified in theory when the tests are independent or positively correlated. In the presence of linkage equilibrium, association tests are independent; in the presence of linkage disequilibrium, they are positively correlated. For a more detailed discussion of the multiple testing issues in SNP studies, see Nyholt (2004)....
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...In the Simes procedure highlighted by Benjamini and Hochberg (1995) in their analysis of FDR, there are n null hypotheses H1,...,Hn and n corresponding P-values P1,...,Pn....
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40,785 citations
"Genome-wide association analysis by..." refers background in this paper
...Contact: klange@ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online....
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...The lasso penalty is an effective device for continuous model selection, especially in problems where the number of predictors p far exceeds the number of observations n (Chen et al., 1998; Claerbout and Muir, 1973; Santosa and Symes, 1986; Taylor et al., 1979; Tibshirani, 1996)....
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13,656 citations
"Genome-wide association analysis by..." refers background in this paper
...Schwender and Ickstadt (2008) and Kooperberg and Ruczinski (2005) identify interactions using logic regression. These and other relevant papers are reviewed by Liang and Kelemen (2008). We focus on a coordinate descent algorithm because it appears to be the fastest available....
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...Schwender and Ickstadt (2008) and Kooperberg and Ruczinski (2005) identify interactions using logic regression....
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9,950 citations
"Genome-wide association analysis by..." refers background in this paper
...Contact: klange@ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online....
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4,339 citations
"Genome-wide association analysis by..." refers background in this paper
...Contact: klange@ucla.edu Supplementary information: Supplementary data are available at Bioinformatics online....
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