Intall SAIGE-QTL using source code https://github.com/weizhou0/qtl

1. Install dependcies

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

2. Download SAIGE-QTL from github

       src_branch=main
       repo_src_url=https://github.com/weizhou0/qtl
       git clone --depth 1 -b $src_branch $repo_src_url	
   

3. Install dependencies: R packages

    Rscript ./qtl/extdata/install_packages.R
           
   

4. Install SAIGE-QTL R package

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

      R CMD INSTALL qtl
     

   • –library=path_to_final_SAIGEQTL_library can be used for specifying the directory where SAIGE-QTL is installed

      R CMD INSTALL --library=path_to_final_SAIGEQTL_library qtl
     

5. Run SAIGE-QTL

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

        library(SAIGEQTL)
   

   to

        library(SAIGEQTL, lib.loc="path_to_final_SAIGEQTL_library")
   

   in the following scripts

    qtl/extdata/makeGroupFile.R
    qtl/extdata/step1_fitNULLGLMM_qtl.R
    qtl/extdata/step2_tests_qtl.R
    qtl/extdata/step3_gene_pvalue_qtl.R