Intall SAIGE using source code https://github.com/saigegit/SAIGE

1. Install dependcies

   • R >= 3.6.1, gcc >= 5.4.0, cmake 3.14.1,

2. Download SAIGE from github

       src_branch=main
       repo_src_url=https://github.com/saigegit/SAIGE
       git clone --depth 1 -b $src_branch $repo_src_url	
   

3. Install dependencies: R packages

    Rscript ./SAIGE/extdata/install_packages.R
           
   

4. Install SAIGE R package

   • To install SAIGE to the root directory storing all R libraries

      R CMD INSTALL SAIGE
     

   • –library=path_to_final_SAIGE_library can be used for specifying the directory where SAIGE is installed

      R CMD INSTALL --library=path_to_final_SAIGE_library SAIGE
     

5. Run SAIGE

   • If SAIGE was not installed in the root R lib path, change

        library(SAIGE)
   

   to

        library(SAIGE, lib.loc="path_to_final_SAIGE_library")
   

   in the following scripts

    SAIGE/extdata/step1_fitNULLGLMM.R
    SAIGE/extdata/step2_SPAtests.R
    SAIGE/extdata/createSparseGRM.R