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/SAIGEQTL
       git clone --depth 1 -b $src_branch $repo_src_url	
   

3. Install dependencies: R packages

    Rscript ./SAIGEQTL/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 SAIGEQTL
     

   • –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 SAIGEQTL
     

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

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

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✅ Next Steps

Installation Complete!

You’ve successfully built SAIGE-QTL from source. Here’s how to get started with your first analysis.

Your Command Prefix

Your scripts are located in:

/path/to/SAIGEQTL/extdata/

Run commands like:

Rscript /path/to/SAIGEQTL/extdata/step1_fitNULLGLMM_qtl.R [options]

💡 Tip: Add to PATH for convenience:

# Add to your ~/.bashrc or ~/.bash_profile
export PATH="/path/to/SAIGEQTL/extdata:$PATH"

# Then you can run:
step1_fitNULLGLMM_qtl.R --help

Quick Start Tutorial

Ready to run your first analysis? Follow this tutorial:

📖 cis-eQTL Analysis Tutorial - Learn how to map local genetic effects on gene expression

What you’ll learn:

• How to prepare your data files
• Running Step 1: Fit the null model
• Running Step 2: Test genetic variants
• Running Step 3: Calculate gene-level p-values

Example command for Source installation users:

Rscript /path/to/SAIGEQTL/extdata/step1_fitNULLGLMM_qtl.R \
    --phenoFile=phenotypes.txt \
    --phenoCol=ENSG00000123456 \
    --traitType=count \
    --outputPrefix=output/gene1

Additional Resources

• Parameters & Options - Complete reference for all command-line parameters
• Running Scripts Guide - Detailed information on running SAIGE-QTL scripts
• FAQ - Common questions and troubleshooting

Need Help?

If you encounter issues:

1. Check the FAQ for common problems
2. Verify R can find the SAIGEQTL library
3. Review the cis-eQTL tutorial for step-by-step guidance