Significance testing in ridge regression for genetic data.
Significance testing in ridge regression for genetic data.
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DOI：
10.1186/1471-2105-12-372
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发表时间：
2011-09-19
影响因子：
3
通讯作者：
De Iorio M
中科院分区：
文献类型：
--
作者：
Cule E;Vineis P;De Iorio M
技术的发展增加了大规模遗传关联研究的可行性。使用SNP阵列、下一代测序技术和插补获得密集型遗传标记。然而，使用这些方法分型的SNP可能由于它们之间的连锁不平衡而高度相关，并且标准的多元回归技术由于它们的高维度和相关结构而无法使用这些数据集。在高维数据的分析中使用惩罚回归的兴趣越来越大。岭回归是一种这样的惩罚回归技术，其不执行变量选择，而是估计每个预测变量的回归系数。因此，需要获得每个岭回归系数的显著性的估计。我们开发和评估岭回归系数的显著性检验。使用模拟研究，我们证明了该测试的性能是可比的排列测试，具有大大降低计算成本的优势。我们引入了p值迹线，这是岭回归系数p值的负对数随收缩参数增加的曲线图，它可以可视化回归系数p值随惩罚增加的变化。我们将所提出的方法应用于肺癌病例对照数据集EPIC，欧洲癌症和营养前瞻性调查。建议的测试是一个有用的替代排列测试的岭回归系数的显著性估计，在大大降低计算成本。p值迹线是一种信息丰富的图形工具，用于评估岭回归系数随着收缩参数增加而显著性检验的结果，并且所提出的检验使其生产在计算上可行。
Technological developments have increased the feasibility of large scale genetic association studies. Densely typed genetic markers are obtained using SNP arrays, next-generation sequencing technologies and imputation. However, SNPs typed using these methods can be highly correlated due to linkage disequilibrium among them, and standard multiple regression techniques fail with these data sets due to their high dimensionality and correlation structure. There has been increasing interest in using penalised regression in the analysis of high dimensional data. Ridge regression is one such penalised regression technique which does not perform variable selection, instead estimating a regression coefficient for each predictor variable. It is therefore desirable to obtain an estimate of the significance of each ridge regression coefficient. We develop and evaluate a test of significance for ridge regression coefficients. Using simulation studies, we demonstrate that the performance of the test is comparable to that of a permutation test, with the advantage of a much-reduced computational cost. We introduce the p-value trace, a plot of the negative logarithm of the p-values of ridge regression coefficients with increasing shrinkage parameter, which enables the visualisation of the change in p-value of the regression coefficients with increasing penalisation. We apply the proposed method to a lung cancer case-control data set from EPIC, the European Prospective Investigation into Cancer and Nutrition. The proposed test is a useful alternative to a permutation test for the estimation of the significance of ridge regression coefficients, at a much-reduced computational cost. The p-value trace is an informative graphical tool for evaluating the results of a test of significance of ridge regression coefficients as the shrinkage parameter increases, and the proposed test makes its production computationally feasible.
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影响因子：
2.1
作者：
Park, Mee Young;Hastie, Trevor
通讯作者：
Hastie, Trevor
影响因子：
30.8
作者：
McKay, James D.;Hung, Rayjean J.;Gaborieau, Valerie;Boffetta, Paolo;Chabrier, Amelie;Byrnes, Graham;Zaridze, David;Mukeria, Anush;Szeszenia-Dabrowska, Neonilia;Lissowska, Jolanta;Rudnai, Peter;Fabianova, Eleonora;Mates, Dana;Bencko, Vladimir;Foretova, Lenka;Janout, Vladimir;McLaughlin, John;Shepherd, Frances;Montpetit, Alexandre;Narod, Steven;Krokan, Hans E.;Skorpen, Frank;Elvestad, Maiken Bratt;Vatten, Lars;Njolstad, Inger;Axelsson, Tomas;Chen, Chu;Goodman, Gary;Barnett, Matt;Loomis, Melissa M.;Lubinski, Jan;Matyjasik, Joanna;Lener, Marcin;Oszutowska, Dorota;Field, John;Liloglou, Triantafillos;Xinarianos, George;Cassidy, Adrian;Zelenika, Diana;Boland, Anne;Delepine, Marc;Foglio, Mario;Lechner, Doris;Matsuda, Fumihiko;Blanche, Helene;Gut, Ivo;Heath, Simon;Lathrop, Mark;Brennan, Paul
通讯作者：
Brennan, Paul
DOI：
10.2307/2987937
发表时间：
1983-01-01
期刊：
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES D-THE STATISTICIAN
影响因子：
--
作者：
ALTMAN, DG;BLAND, JM
通讯作者：
BLAND, JM
影响因子：
2.5
作者：
HOERL, AE;KENNARD, RW
通讯作者：
KENNARD, RW
影响因子：
4.5
作者：
Hoggart, Clive J.;Whittaker, John C.;De Iorio, Maria;Balding, David J.
通讯作者：
Balding, David J.