cv.interep: k-folds cross-validation for interep

In interep: Interaction Analysis of Repeated Measure Data

k-folds cross-validation for interep

Description

This function does k-fold cross-validation for interep and returns the optimal value of lambda.

Usage

cv.interep(e, g, y, beta0, lambda1, lambda2, nfolds, corre, pmethod, maxits)

Arguments

e	matrix of environment factors.
g	matrix of omics factors. In the case study, the omics measurements are lipidomics data.
y	the longitudinal response.
beta0	the intial value for the coefficient vector.
lambda1	a user-supplied sequence of \lambda_{1} values, which serves as a tuning parameter for individual predictors.
lambda2	a user-supplied sequence of \lambda_{2} values, which serves as a tuning parameter for interactions.
nfolds	the number of folds for cross-validation.
corre	the working correlation structure that is used in the estimation algorithm. interep provides three choices for the working correlation structure: "a" as AR-1", "i" as "independence" and "e" as "exchangeable".
pmethod	the penalization method. "mixed" refers to MCP penalty to individual main effects and group MCP penalty to interactions; "individual" means MCP penalty to all effects.
maxits	the maximum number of iterations that is used in the estimation algorithm.

Details

When dealing with predictors with both main effects and interactions, this function returns two optimal tuning parameters, \lambda_{1} and \lambda_{2}; when there are only main effects in the predictors, this function returns \lambda_{1}, which is the optimal tuning parameter for individual predictors containing main effects.

Value

an object of class "cv.interep" is returned, which is a list with components:

lam1	the optimal \lambda_{1}.
lam2	the optimal \lambda_{2}.

References

Zhou, F., Ren, J., Li, G., Jiang, Y., Li, X., Wang, W.and Wu, C. (2019). Penalized variable selection for Lipid–environment interactions in a longitudinal lipidomics study. Genes, 10(12), 1002

Zhou, F., Ren, J., Liu, Y., Li, X., Wang, W.and Wu, C. (2022). Interep: An r package for high-dimensional interaction analysis of the repeated measurement data. Genes, 13(3): 554 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3390/genes13030544")}

Zhou, F., Ren, J., Lu, X., Ma, S. and Wu, C. (2021) Gene–Environment Interaction: a Variable Selection Perspective. Epistasis: Methods and Protocols, 191-223

Ren, J., Zhou, F., Li, X., Chen, Q., Zhang, H., Ma, S., Jiang,Y. and Wu, C. (2020). Semi-parametric Bayesian variable selection for Gene-Environment interactions. Statistics in Medicine, 39(5): 617-638 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.8434")}

Wu, C., Zhou, F., Ren, J., Li, X., Jiang, Y., Ma, S. (2019). A Selective Review of Multi-Level Omics Data Integration Using Variable Selection. High-Throughput, 8(1) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.3390/ht8010004")}

Ren, J., Du, Y., Li, S., Ma, S., Jiang, Y. and Wu, C. (2019). Robust network-based regularization and variable selection for high-dimensional genomic data in cancer prognosis. Genetic epidemiology, 43(3), 276-291 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/gepi.22194")}

Ren, J., Jung, L., Du, Y., Wu, C., Jiang, Y. and Liu, J. (2019). regnet: Network-Based Regularization for Generalized Linear Models. R package, version 0.4.0

Wu, C., Zhang, Q., Jiang, Y. and Ma, S. (2018). Robust network-based analysis of the associations between (epi) genetic measurements. Journal of multivariate analysis, 168, 119-130 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.jmva.2018.06.009")}

Wu, C., Zhong, P.-S., and Cui, Y. (2018). Additive varying-coefficient model for nonlinear gene-environment interactions. Statistical Applications in Genetics and Molecular Biology, 17(2) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1515/sagmb-2017-0008")}

Wu, C., Jiang, Y., Ren, J., Cui, Y., Ma, S. (2018). Dissecting gene-environment interactions: A penalized robust approach accounting for hierarchical structures. Statistics in Medicine, 37: 437–456 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.7518")}

Ren, J., He, T., Li, Y., Liu, S., Du, Y., Jiang, Y. and Wu, C. (2017). Network-based regularization for high dimensional SNP data in the case–control study of Type 2 diabetes. BMC genetics, 18(1), 44 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1186/s12863-017-0495-5")}

Jiang, Y., Huang, Y., Du, Y., Zhao, Y., Ren, J., Ma, S., & Wu, C. (2017). Identification of prognostic genes and pathways in lung adenocarcinoma using a Bayesian approach. Cancer Inform, 1(7) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1177/1176935116684825")}

Wu, C., and Ma, S. (2015). A selective review of robust variable selection with applications in bioinformatics. Briefings in Bioinformatics, 16(5), 873–883 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bib/bbu046")}

Wu, C., Shi, X., Cui, Y. and Ma, S. (2015). A penalized robust semiparametric approach for gene-environment interactions. Statistics in Medicine, 34 (30): 4016–4030 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.6609")}

Wu, C., Cui, Y., and Ma, S. (2014). Integrative analysis of gene–environment interactions under a multi–response partially linear varying coefficient model. Statistics in Medicine, 33(28), 4988–4998 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/sim.6287")}

Wu, C. and Cui, Y. (2013). A novel method for identifying nonlinear gene–environment interactions in case–control association studies. Human Genetics, 132(12):1413–1425 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s00439-013-1350-z")}

Wu, C. and Cui, Y. (2013). Boosting signals in gene–based association studies via efficient SNP selection. Briefings in Bioinformatics, 15(2):279–291 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1093/bib/bbs087")}

Wu, C., Zhong, P.S. and Cui, Y. (2013). High dimensional variable selection for gene-environment interactions. Technical Report, Michigan State University.

Wu, C., Li, S., and Cui, Y. (2012). Genetic Association Studies: An Information Content Perspective. Current Genomics, 13(7), 566–573 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.2174/138920212803251382")}

interep documentation built on May 29, 2024, 8:52 a.m.