Gene Environment Interaction Estimator
Project description
RHE
Randomized Haseman–Elston regression for Multi-variance Components: Python wrappers for Gene-ENviroment Interaction Estimator
Installation
pip install rhe
This package provides basic Python wrappers for the GENIE executables. Full documentation for the GENIE project, as well as sample data necessary to run the toy examples below, is available here: https://github.com/sriramlab/GENIE
Interface
This package provides the following functions:
rhe.run_genie
rhe.run_genie_mem
rhe.run_genie_multi_pheno
Run GENIE with a list of command line arguments
from rhe import run_genie
gen = 'path/to/test'
phen = 'path/to/test.pheno'
covar = 'path/to/test.cov'
annot = 'path/to/single.annot'
env = 'path/to/test.env'
run_genie(
['-g', gen, '-p', phen, '-c', covar, '-e', env, '-m', 'G+GxE+NxE', '-k', '10', '-jn', '10', '-o',
'path/to/analysis.out', '-annot', annot, '-t', '6']
)
Run GENIE with a single string of command line arguments
from rhe import run_genie
gen = 'path/to/test'
phen = 'path/to/test.pheno'
covar = 'path/to/test.cov'
annot = 'path/to/single.annot'
env = 'path/to/test.env'
run_genie(
f'-g {gen} -p {phen} -c {covar} -e {env} -m G+GxE+NxE -k 10 -jn 10 -o path/to/analysis.out -annot {annot} -t 6'
)
Run GENIE with using a config file
from rhe import run_genie_mem
with open('config.txt', 'w') as f:
f.write('genotype=path/to/test\n')
f.write('phenotype=path/to/test.pheno\n')
f.write('covariate=path/to/test.cov\n')
f.write('environment=path/to/test.env\n')
f.write('annotation=path/to/single.annot\n')
f.write('output=path/to/test.py.list.3.out\n')
f.write('nthreads=6\n')
f.write('num_vec=20\n')
f.write('num_jack=10\n')
f.write('trace=1\n')
f.write('model=G\n')
f.write('verbose=1\n')
run_genie_mem(
['--config', 'config.list.txt']
)
Citation
1. Ali Pazokitoroudi, Andrew Dahl, Noah Zaitlen, Saharon Rosset, Sriram Sankararaman.
bioRxiv 2023.12.12.571316; doi: https://doi.org/10.1101/2023.12.12.571316
2. Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Aaron Zhou,
Bogdan Pasaniuc, Sriram Sankararaman. Nature Communications (2020); doi: https://doi.org/10.1101/522003
Version
v1.0.0
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