Skip to contents

HierFabs: installation

Xiao Zhang

2022-10-22

Source: vignettes/HierFabs.Rmd
HierFabs.Rmd

Introduce the HierFabs

This vignette provides an introduction to the R package HierFabs, where the function HierFabs implements our model.

  • With the completely newly developed forward and backward steps to accommodate hierarchy, HierFabs is able to detect important main effects and interactions under both the strong and weak hierarchy. User can specify the hierarchy constraint by parameter hier.
  • Advancing from the existing studies, HierFabs accommodates multiple types of interaction models with differentiable loss functions under a unified framework. For now, HierFabs supports linear mdoel, Cox model, quantile model and logistic model. User can specify the model by parameter model.
  • HierFabs can be applied for both gene-gene interaction analysis and gene-environment interaction analysis. Which type of analysis is used depends on whether environmental variables are provided.
  • HierFabs is observed to be highly computational efficient. It uses a warm-start strategy to update coefficients and a data-driven approach to update tuning parameter.

Install the HierFabs

The package can be installed with the following command from Github:

install.packages('devtools')
devtools::install_github("XiaoZhangryy/HierFabs")

The package can be loaded with the command:

Report issues

If someone have any problem or suggestion, welcom to go there to create an issue.

Session information 

sessionInfo()
#> R version 4.1.3 (2022-03-10)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 19043)
#> 
#> Matrix products: default
#> 
#> locale:
#> [1] LC_COLLATE=English_United States.1252 
#> [2] LC_CTYPE=English_United States.1252   
#> [3] LC_MONETARY=English_United States.1252
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.1252    
#> system code page: 936
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] rprojroot_2.0.3   digest_0.6.29     R6_2.5.1          jsonlite_1.8.2   
#>  [5] magrittr_2.0.3    evaluate_0.15     stringi_1.7.8     rlang_1.0.6      
#>  [9] cachem_1.0.6      cli_3.2.0         rstudioapi_0.13   fs_1.5.2         
#> [13] jquerylib_0.1.4   bslib_0.4.0       ragg_1.2.2        rmarkdown_2.13   
#> [17] pkgdown_2.0.6     textshaping_0.3.6 desc_1.4.1        tools_4.1.3      
#> [21] stringr_1.4.1     purrr_0.3.4       yaml_2.3.5        xfun_0.30        
#> [25] fastmap_1.1.0     compiler_4.1.3    systemfonts_1.0.4 memoise_2.0.1    
#> [29] htmltools_0.5.3   knitr_1.38        sass_0.4.2