struct-lmm 0.0.20

Linear mixed model to study multivariate genotype-environment interactions

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

norm_env  --in $EFILE0 --out $EFILE

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.

Authors

• Rachel Moore - https://github.com/rm18

• Danilo Horta - https://github.com/horta

• Francesco Paolo Casale - https://github.com/fpcasale

License

This project is licensed under the Apache License (Version 2.0, January 2004) - see the LICENSE file for details