Abstract：
BACKGROUND AND OBJECTIVE:Univariate feature selection is one of the simplest and most commonly used techniques to develop a multigene predictor for survival. Presently, there is no software tailored to perform univariate feature selection and predictor construction. METHODS:We develop the compound.Cox R package that implements univariate significance tests (via the Wald tests or score tests) for feature selection. We provide a cross-validation algorithm to measure predictive capability of selected genes and a permutation algorithm to assess the false discovery rate. We also provide three algorithms for constructing a multigene predictor (compound covariate, compound shrinkage, and copula-based methods), which are tailored to the subset of genes obtained from univariate feature selection. We demonstrate our package using survival data on the lung cancer patients. We examine the predictive capability of the developed algorithms by the lung cancer data and simulated data. RESULTS:The developed R package, compound.Cox, is available on the CRAN repository. The statistical tools in compound.Cox allow researchers to determine an optimal significance level of the tests, thus providing researchers an optimal subset of genes for prediction. The package also allows researchers to compute the false discovery rate and various prediction algorithms.
journal_name
Comput Methods Programs Biomedjournal_title
Computer methods and programs in biomedicineauthors
Emura T,Matsui S,Chen HYdoi
10.1016/j.cmpb.2018.10.020subject
Has Abstractpub_date
2019-01-01 00:00:00pages
21-37eissn
0169-2607issn
1872-7565pii
S0169-2607(18)30422-Xjournal_volume
168pub_type
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章,meta分析
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
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journal_title：Computer methods and programs in biomedicine
pub_type： 杂志文章
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