# Saige package for R

SAIGE is an R package (opens new window) with Scalable and Accurate Implementation of Generalized mixed model (Chen, H. et al. 2016). It accounts for sample relatedness and is feasible for genetic association tests in large cohorts and biobanks.

Install using conda
Install the hard way

TIP

If you are interested in using Saige, you should try to Regenie, a strong C++ tool for whole genome regression modelling of large GWAS.

# Install using conda

Requirements

Conda (miniconda), see our Conda tutorial for more details.
Conda channels: conda-forge, bioconda

You will need bioconda and conda-forge channels. If you have not set channels yet make sure to add them in this order:

conda config --add channels bioconda
conda config --add channels conda-forge

To create a new environment and install the latest version of SAIGE use:

conda create -n saige -c bioconda r-saige=0.44.2
conda activate saige

After installation you should be able to import SAIGE library in R and run SAIGE scripts:

step1_fitNULLGLMM.R --help
step2_SPAtests.R --help
createSparseGRM.R --help

If you need to run your scripts with older version of R, you can use 3.6.3:

conda install -c conda-forge -c bioconda "r-base=3.6.3" r-saige

# Install the hard way

The below guide is based on packages listed in the Dockerfile example in Github. It describes installation of the SAIGE R package (opens new window) on a clean IAAS or BLUE machine in HUNT Cloud.

Requirements

Ubuntu operating system (current installation is tested on 18.04).
Administrator privileges (HUNT IAAS or HUNT BLUE machines).
Fresh coffee and 30 minutes to spare.

# Defining your software directory

Below is an example:

# Define your software directory
software_dir="/home/ubuntu/software/"

# Create directory if it don't exist
mkdir -p $software_dir

# Move into the directory
cd $software_dir

# Install required APT packages

sudo apt update -y && sudo apt-get install -y \
    build-essential \
    cmake \
    curl \
    libboost-all-dev \
    libbz2-dev \
    libcairo2-dev \
    libcurl4-openssl-dev \
    liblzma-dev \
    libopenblas-dev \
    libpcre3-dev \
    libpng-dev \
    libreadline-dev \
    libssl-dev \
    libz-dev \
    python3-pip \
    python3-setuptools \
    unzip \
    gfortran \
    r-cran-rjava \
    openjdk-8-jdk

# Defining your Java version

Run the code below and manually choose java-8in the provided list and hit 'ENTER'.

# manual update to java-8-openjdk
sudo update-alternatives --config java

# Installing required python packages

pip3 install cget;

# Installing a specific R version

The current SAIGE version requires a specific R-version (3.5.1). The below snippets compile this specific version.

# ensure software dir
cd $software_dir

# define version
r_version="3.5.1";

# download
curl -O https://cloud.r-project.org/src/base/R-3/R-${r_version}.tar.gz;

# unzip
tar xvzf R-${r_version}.tar.gz;

# cleanup
rm R-${r_version}.tar.gz;

# move into r-folder
cd $software_dir/R-${r_version}

# configure
sudo ./configure \
  --with-x=no \
  --with-blas="-lopenblas" \
  --enable-R-shlib  \
  -enable-shared;

# make
sudo make; # TODO stopped here
sudo mkdir -p /usr/local/lib/R/lib;

# install
sudo make install;

# cleanup
cd $software_dir
sudo rm -rf $software_dir/R-${r_version}

# Installing SAIGE

cd $software_dir

# Download latest version
curl -OL https://github.com/weizhouUMICH/SAIGE/archive/master.zip

# Unpack
unzip master.zip

# Update file folder names
mv SAIGE-master/ SAIGE/

# Install required R-packages
Rscript SAIGE/extdata/install_packages.R

# Install SAIGE
R CMD INSTALL SAIGE

# Set number of threads for openblas

This steps adds a thread restriction on BLAS to avoid multithread conflicts with other R packages.

First, add restriction to step2_SPAtests.R

echo "#!/usr/bin/env Rscript

# Restrict threads in openblas
hasOpenBlas = grepl(\"openblas\",extSoftVersion()[\"BLAS\"]);
if (hasOpenBlas) {
  ### Only when using openblas instead of blas
  require(inline)
  openblas.set.num.threads <- cfunction( signature(ipt=\"integer\"),
    body = \'openblas_set_num_threads(*ipt);\',
    otherdefs = c (\'extern void openblas_set_num_threads(int);\'),
      libargs = c (\'-L/opt/openblas/lib -lopenblas\'),
      language = \"C\",
      convention = \".C\")};
if (hasOpenBlas) openblas.set.num.threads(1)
" > insert_openblas_restriction.tmp

Then, add to file:

# cut header
cat SAIGE/extdata/step2_SPAtests.R | sed -n '1!p' > step2_body.tmp

# Combine

cat insert_openblas_restriction.tmp \
    step2_body.tmp > step2_SPAtests.R
Install the required 'inline' R-package:
echo 'req_packages <- "inline";
for (pack in req_packages) {
  if(!require(pack,character.only = TRUE)) {
    install.packages(pack, repos = "http://cran.us.r-project.org")}}' \
> install_inline.R
Rscript install_inline.R
rm install_inline.R

Add quick references:

# Move files to usr/local/bin for quick referencing
sudo mv SAIGE/extdata/step1_fitNULLGLMM.R /usr/local/bin/
sudo mv step2_SPAtests.R /usr/local/bin/
sudo mv SAIGE/extdata/createSparseGRM.R /usr/local/bin/
sudo chmod a+x /usr/local/bin/*.R

# Cleanup

rm -rf master.zip
rm -rf SAIGE
rm insert_openblas_restriction.tmp
rm step2_body.tmp
rm step2_SPAtests.R

# Testing SAIGE

step1_fitNULLGLMM.R

step2_SPAtests.R

createSparseGRM.R

More information

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