LASSO

Parameters

-l flag for LASSO run

--p_in_expr_target log2 fold-changes of expression levels of the target genes. A .tsv file, rows and columns are indexed by the target gene ids and sample ids

--p_in_expr_reg log2 fold-changes of expression levels of the regulators. A .tsv file, rows and columns are indexed by the regulator ids and sample ids.

--flag_global_shrinkage "ON" for global shrinkage, "OFF" otherwise (default OFF).

--flag_local_shrinkage "ON" for not using the global shrinkage, "OFF" otherwise (default ON).

--lasso_nbr_fold number of CV for selecting optimal lambda (default 10). This parameter works only if flag_global_shrinkage is "ON".

--flag_microarray "MICROARRAY" for microarray expression data, "RNA-SEQ" for RNA-Seq data.

--p_out_dir path of the output directory NetProphet results.

--lasso_slurm_nodes number of nodes used for running each fold of CV. This parameter works only if flag_slurm is "ON".

--lasso_slurm_mem memory used for the SLURM run. This parameter works only if flag_slurm is "ON".

--p_src_code path of the source code of NetProphet.

Command

p_wd=/scratch/mblab/dabid/proj_net/
p_src_code=${p_wd}code/NetProphet_3.0/
p_out_dir=${p_wd}code/NetProphet_3.0/toy_example/res/features/

${p_src_code}np3 -l \
    --flag_global_shrinkage ON \
    --p_in_expr_target ${p_src_code}toy_example/data_zev_expr_500_100_indexed \
    --p_in_expr_reg ${p_src_code}toy_example/data_zev_expr_reg_50_100_indexed \
    --p_out_dir ${p_out_dir} \
    --flag_singularity OFF \
    --flag_slurm ON \
    --p_out_dir_logs ${p_out_dir}log/ \
    --data toy_example