Linear mixed model to study multivariate genotype-environment interactions
Project description
Structured Linear Mixed Model (StructLMM) is a computationally efficient method to test for and characterize loci that interact with multiple environments.
Getting Started
StructLMM is Python package implemented in both Python and R programming languages that depends on some libraries implemented in C. To make its installation as easy as possible, we make use conda, a package manager for software implemented in Python, R, and C/C++ (among others) languages.
Interaction with StructLMM happens in the terminal via the following command line tools installed with the package, and described at the Command Line Interface section of the documentation:
norm_env
struct_lmm_analyze
lmm_int_analyze
lmm_analyze
struct_lmm_analyze
Requisites
The installation script runs in on GNU/Linux and macOS operating systems. It requires either wget or curl command line tools in case conda is not already installed. In any case, the installation script will inform the user if it cannot proceed. Otherwise, the StructLMM dependencies is automatically installed and does not require user intervention.
Install
For Linux and macOS operating systems, struct-lmm can be install from the command line by entering
bash <(curl -fsSL https://raw.githubusercontent.com/limix/struct-lmm/master/install)
The user might be prompted to install conda in case he/she does not have it, and will warn the user if for some reason the installation process cannot proceed. The whole installation process should take less than 15 minutes and mainly consists in downloading essential R and Python packages for a working environment.
Usage example
StructLMM can be run from the command line using the following
wget http://www.ebi.ac.uk/~casale/data_structlmm.zip
unzip data_structlmm.zip
BFILE=data_structlmm/chrom22_subsample20_maf0.10
PFILE=data_structlmm/expr.csv
EFILE0=data_structlmm/env.txt
EFILE=data_structlmm/env_norm.txt
struct_lmm_analyze --bfile $BFILE --pfile $PFILE --pheno_id gene10 --efile $EFILE --ofile out/results.res --idx_start 0 --idx_end 1000 --batch_size 100 --unique_variants
Further examples can be found at http://struct-lmm.readthedocs.io/.
Documentation
Documentation is available online at http://struct-lmm.readthedocs.io/.
Problems
If you encounter any problem, please, consider submitting a new issue.
License
This project is licensed under the Apache License (Version 2.0, January 2004) - see the LICENSE file for details
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