the Precision Lasso
Implementation of the Precision Lasso in this paper:
''Wang H, Lengerich BJ, Aragam B, Xing EP. Precision Lasso: Accounting for Correlations and Linear Dependencies in High-Dimensional Genomic Data. Bioinformatics. 2017''
the Precision Lasso is a Lasso variant that is showed to work better compared to other Lasso variants in terms of variable selection when there are correlated and linearly dependent variables existing.
- models/ main method for the Precision Lasso
- utility/ other helper files
- runPL.py main entry point of using the Precision Lasso to work with your own data
An Example Command:
python runPL.py -t csv -n data/toy
- Precision Lasso currently supports CSV and binary PLINK files.
- Extensions to other data format can be easily implemented through
utility/dataLoadear. Feel free to contact us for the support of other data format.
You will need to have numpy and scipy installed on your current system. You can install precision lasso using pip by doing the following
pip install git+https://github.com/HaohanWang/thePrecisionLasso
You can also clone the repository and do a manual install.
git clone https://github.com/HaohanWang/thePrecisionLasso python setup.py install
Software with GUI
Software with GUI will be avaliable through GenAMap
Proficient python users can directly call the Precision Lasso with python code, see the example here