CKLRT

Composite Kernel Machine Regression Based on Likelihood Ratio Test

Composite Kernel Machine Regression based on Likelihood Ratio Test (CKLRT): in this package, we develop a kernel machine regression framework to model the overall genetic effect of a SNP-set, considering the possible GE interaction. Specifically, we use a composite kernel to specify the overall genetic effect via a nonparametric function and we model additional covariates parametrically within the regression framework. The composite kernel is constructed as a weighted average of two kernels, one corresponding to the genetic main effect and one corresponding to the GE interaction effect. We propose a likelihood ratio test (LRT) and a restricted likelihood ratio test (RLRT) for statistical significance. We derive a Monte Carlo approach for the finite sample distributions of LRT and RLRT statistics. (N. Zhao, H. Zhang, J. Clark, A. Maity, M. Wu. Composite Kernel Machine Regression based on Likelihood Ratio Test with Application for Combined Genetic and Gene-environment Interaction Effect (Submitted).)

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Description file content

Package
CKLRT
Type
Package
Title
Composite Kernel Machine Regression Based on Likelihood Ratio Test
Version
0.2.3
Author
Ni Zhao [aut], Haoyu Zhang [aut, cre]
Maintainer
Haoyu Zhang
Description
Composite Kernel Machine Regression based on Likelihood Ratio Test (CKLRT): in this package, we develop a kernel machine regression framework to model the overall genetic effect of a SNP-set, considering the possible GE interaction. Specifically, we use a composite kernel to specify the overall genetic effect via a nonparametric function and we model additional covariates parametrically within the regression framework. The composite kernel is constructed as a weighted average of two kernels, one corresponding to the genetic main effect and one corresponding to the GE interaction effect. We propose a likelihood ratio test (LRT) and a restricted likelihood ratio test (RLRT) for statistical significance. We derive a Monte Carlo approach for the finite sample distributions of LRT and RLRT statistics. (N. Zhao, H. Zhang, J. Clark, A. Maity, M. Wu. Composite Kernel Machine Regression based on Likelihood Ratio Test with Application for Combined Genetic and Gene-environment Interaction Effect (Submitted).)
License
GPL-3
Depends
R (>= 3.1.0),
Imports
Rcpp (>= 0.12.17), mgcv, MASS, nlme, compiler, stats
LinkingTo
RcppEigen, Rcpp
Encoding
UTF-8
LazyData
true
RoxygenNote
6.0.1
NeedsCompilation
yes
Packaged
2018-09-13 21:00:37 UTC; haoyuzhang
Repository
CRAN
Date/Publication
2018-09-13 21:40:02 UTC

install.packages('CKLRT')

0.2.3

2 months ago

Haoyu Zhang

GPL-3

Depends on

R (>= 3.1.0),

Imports

Rcpp (>= 0.12.17), mgcv, MASS, nlme, compiler, stats

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