solarius
R package to interface SOLAR
R package to interface SOLAR
SOLAR performs likelihood ratio test (LRT)
to evaluate the significance of covariates in a model.
covtest argument says to conduct the LRT tests for all covariates.
This option is disabled by default (to save calculation time).
mod1 <- solarPolygenic(trait1 ~ age + sex, dat30)
mod1$cf
## covariate Estimate SE Chi pval
## 1 age 0.0004591 0.01484 NA NA
## 2 sex -0.4559509 0.31251 NA NA
For the next model the test results are collected into cf slot
of the model object.
mod2 <- solarPolygenic(trait1 ~ age + sex, dat30, covtest = TRUE)
mod2$cf
## covariate Estimate SE Chi pval
## 1 age 0.0004591 0.01484 0.001 0.9753
## 2 sex -0.4559509 0.31250 2.118 0.1455
The SOLAR command was the following.
mod2$solar$cmd
## [1] "trait trait1"
## [2] "covariate age sex"
## [3] ""
## [4] "polygenic -prob 0.05 -screen -all"
In particular, -screen -all options for polygenic command do the job.
These two options say to screen the covariates, although all covariates will be saved (not screened).
That leads to the tests without covariate screening.
SOLAR generates files to store the modeling results.
names(mod2$solar$files$model)
## [1] "last.mod" "noage.mod"
## [3] "noage.out" "nocovar.mod"
## [5] "nocovar.out" "nosex.mod"
## [7] "nosex.out" "null0.mod"
## [9] "null0.out" "out.covariate"
## [11] "out.globals" "out.param.univar"
## [13] "out.varcomp.univar" "p0.mod"
## [15] "p0.out" "polygenic.logs.out"
## [17] "polygenic.out" "polygenic.residuals"
## [19] "polygenic.residuals.stats" "poly.mod"
## [21] "poly.out" "s0.mod"
## [23] "s0.out" "spor.mod"
## [25] "spor.out"
Files noage.mod and nosex.mod are two polygenic models without one of the two covariates,
which in turn were compared to the null model with all covariates to get the LRT statistics.