Evaluating a Linear model

Please clone this repo in the DeepGP folder.

git clone https://github.com/lauzingaretti/DeepGP.git DeepGP

Make sure you have the dependencies installed. To install dependencies, please run in bash the following command:

pip3 install -r requirements.txt

usually as sudoer.

Go to the Project main folder:

cd DeepGP

Prepare the output folder where results should be stored:

mkdir /path/to/output/Folder

Runing Ridge regression by type in bash:

python3 Deep_genomic.py --Xtr /dataset_wheat/XWheatTrain.csv --ytr /dataset_wheat/YWheatTrain.csv --Xval /dataset_wheat/XWheatVal.csv --yval /dataset_wheat/YWheatVal.csv --ridge
Alternatively, you can run lasso by:

python3 Deep_genomic.py --Xtr /dataset_wheat/XWheatTrain.csv --ytr /dataset_wheat/YWheatTrain.csv --Xval /dataset_wheat/XWheatVal.csv --yval /dataset_wheat/YWheatVal.csv --lasso

Once the running process finished, go to /path/to/output/Folder and in a folder called ridge or lasso respectively you can find the figures and predictive abilities.

Note that it can evaluate both diploids and polyploids organisms and although we are not interested in linear models themselves, we implement them in order to compare them with Dep architectures.