Expression correlation threshold for gene pairs

[dariotommasini]

Hi @atarashansky ,

I hope you're doing well! I was looking through the documentation for a way to set the expression correlation threshold for finding gene pairs. I came across the w1t and w2t arguments, but I'm not sure if they are the right ones. I expected there to only be one threshold, not two. Do you know if this the expression correlation threshold?

Also, I noticed that in the _find_link_genes_avg function, the w1t/w2t argument is never used. Should w1t be used in place of 0.2 on line https://github.com/atarashansky/SAMap/blob/main/samap/analysis.py#L813 ?

Thank you for the help!

Dario