Table of Contents

• Introduction
• Citation
• How to install and run GATE
• UK Biobank GWAS Results
• Log for fixing bugs
• Notes for users before running jobs

Introduction

Current version is 0.45

GATE (Genetic Analysis of Time-to-Event phenotypes) is an R package with Scalable and accurate genome-wide association analysis of censored survival data in large scale biobanks using frailty models.

GATE performs single-variant association tests for time-to-event endpoints. GATE uses uses the saddlepoint approximation (SPA)(mhof, J. P. , 1961; Kuonen, D. 1999; Dey, R. et.al 2017) to account for heavy censoring rates.

GATE is based on joint work by Rouank Dey and Wei Zhou.

Citation

How to install and run GATE (Similar to SAIGE and SAIGE-GENE)

https://github.com/weizhouUMICH/SAIGE/wiki/Genetic-association-tests-using-SAIGE

The docker image can be found in the docker hub wzhou88/saige.survival:0.44.1

Notes for users before running jobs

• After installation, the package needs to be called as SAIGE (will update)

• Currently, the only difference between this and the regular SAIGE job is that for step1, two additional arguments are used

eventTimeCol = “”,
eventTimeBinSize = 1

traitType = “survival”

eventTimeCol is the column name for the event time, e.g. age of diagnosis eventTimeBinSize is used to set the bin size for evene times. eventTimeBinSize=1 means the bin size will be 1 and if eventTimeBinSize is not specified, raw event time values will be used. phenoCol is for event status (0 or 1 is for censored or event)

Logs for bug fixing

• 0.45 (June-30-2023) check perfect seperation after expanding the factor covariates. fix the Error in solve.default(t(X1) %*% (X1 * V))

• 0.44.1 (June-15-2023) changed the package name to GATE from SAIGE

• 0.44.1 (December-20-2022) fixed the error X1_fg %*% Z : non-conformable argument

• 0.42.1 (August-19-2021) trying to fix the error X1_fg %*% Z : non-conformable argument

• 0.42 (July-14-2021) fix the "AF > 0.5" error when input file is VCF

• 0.41 (January-11-2021) fix the error from the merging branches

Installation

Install GATE using the conda environment

0. Download and install miniconda

1. Create a conda environment using

   • conda environment file is in the SAIGE folder: https://github.com/weizhou0/GATE/conda_env/environment-RSAIGE_v0.yml

   • After downloading environment-RSAIGE_v0.yml, run following command

   conda env create -f environment-RSAIGE_v0.yml
   

2. Activate the conda environment RSAIGE_v0

     conda activate RSAIGE_v0
     FLAGPATH=`which python | sed 's|/bin/python$||'`
     export LDFLAGS="-L${FLAGPATH}/lib"
     export CPPFLAGS="-I${FLAGPATH}/include"
   

3. Install zlib

   • download zlib and install zlin following the link
   • add the path to the zlib.h to ~/.bashrc

     export PATH=path_to_zlib:$PATH  
   

   • activate ~/.bashrc, you may need to log out and log in the system

     source ~/.bashrc
   

4. Install GATE from the source code

     src_branch=main
   
     repo_src_url=https://github.com/weizhou0/GATE
     git clone --depth 1 -b $src_branch $repo_src_url
     Rscript ./GATE/extdata/install_packages_v0.R
     R CMD INSTALL --library=path_to_final_GATE_library GATE
   

   When call GATE in R, set lib.loc=path_to_final_GATE_library.

     library(GATE, lib.loc=path_to_final_GATE_library)