LASSO penalty issue in customized gene activity score calculation

[wangmeijiao]

Hi,

I understand that in the script scATAC_04_Compute_Gene_Scores.R, gene activity scores are calculated by the custom_cicero_cds function in a more efficient way and at the same time cell grouping information is kept for next steps (that is great!). It seems to me that unlike the original cicero paper method, the following codes ignores the peak-gene distance penalty but directly calculates the coaccessibility correlation and others. I wonder if I miss something or it does not matter to skip the distant penalty issue. My question: is there any difference if the peak-gene distance variable is considered? This is important to fully understand the gene activity score, so I am looking forward to hear from your suggestion.

Cheers, Meijiao