• Unfinished project. Version now is 0.0.1

• R: version > 3.6.0, packages: "genio", "glmnet"
• Python: packages: "pandas-plink"

• For testing, run elasnet_generation.R. For example, Rscript elasnet_generation.R test test.frq annotation_Whole_Blood.txt gamma.txt expression.txt true_evaluation.txt 0.05 0.1 0.05 0.1

  The first argument is plink file location, second is frequency file location, third is annotation file location, fourth is initialized gamma output file location, fifth is gene expression output file location, sixth argument is expected evaluation results, seventh argument is total heritability, eighth argument is percentage of rare variants heritability, nineth argument is percentage of gamma=1, last argument is heritability of annotation.

• Then run read_data_elasnet.py. For example, python read_data_elasnet.py --plink test --expression expression.txt --gamma gamma.txt --frq test.frq --annotation annotation_Whole_Blood.txt --outSNP SNP.txt --outAnno anno.txt --outPerfer pre_evaluation.txt

  The first argument is plink file location, second is gene expression file location, third is initialized gamma file location which should be the result in the first step, fourth is frequency file location, fifth is annotation file location, sixth is SNP's coefficient output file location, seventh is annotation's coefficient output file location, the last one is predicted evaluation results.

This package is still on going.

CRAG's source-code repository is hosted here on GitHub.

CRAG