Imputation Methods Comparison

The idea of our project is to create a platform a platform for comparison of imputation methods of gene expression. Currently we support an user friendly GUI interface for the following imputation methods:

• MetaXcan
• Fusion
• Tigar

Demo

Installation

The installation was tested on Ubuntu18.04. Requirements:

• R language
• anaconda
• git

Download this repository from github, then:

conda environments

Open the project directory imputation_methods_comparison in the terminal and execute the following commands:

cd conda_env
conda env create -f main.yml
conda env create -f metaxcan.yml
conda env create -f tigar.yml

Optional conda installation commands, not necessary for a basic usage:

conda env create -f ldsc.yml
conda env create -f second.yml

R environment (for Fusion only)

The installation process for R environment is identical as provided by authors of Fusion software More information about installation

Plink library

At the beginning download and unpack the plink library

wget https://github.com/gabraham/plink2R/archive/master.zip
unzip master.zip

Plink library has two dependencies. On Ubuntu18.04 we installed them with the following commands:

• sudo apt-get install r-cran-rcppeigen alternatively try: install.packages(c('RcppEigen', 'digest'))
• Type R and paste:install.packages('Rcpp')

Type R in and install plink install.packages('plink2R-master/plink2R/',repos=NULL)

Other dependencies

Type R and install:

install.packages(c('optparse','RColorBrewer'))
install.packages("corrplot")
install.packages(c('glmnet','methods'))

Tigar dependencies

Install tabix and bgzip. We used the following command:

sudo apt-get install -y tabix

Project dependencies

Open file imputation_methods_comparison/definitions.py. Update CONDA variable in this file, if a path to conda.sh file in your system is different.

Add path to imputation_methods_comparison directory to your PYTHONPATH. In order to do it, you should add similar line to the end of our /home/username/.bashrc file:

export PYTHONPATH="${PYTHONPATH}:/home/username/Desktop/imputation_methods_comparison"

Run

Open project directory imputation_methods_comparison in the terminal and type:

conda activate main
python main.py

FAQ installation and usage (Ubuntu18.04)

• To complete installing conda environments, you may need to run sudo apt-get install gcc python3-dev
• python main.py does not start, because of QT5 problem . Try: sudo apt-get install --reinstall libxcb-xinerama0
• When you run an imputation method and see LINE 19: 123456 Killed check system logs in /var/log/syslog. Probably you have too little RAM on your machine and kernel stops the bash script. A solution for this issue could be creating a swap file
• To develop our project you may need to install git-lfs, however for normal usage it is unnecessary.