search

kmayerb / tcrdist3

flexible CDR based distance metrics
MIT License
53 stars 17 forks source link

Guidance on using find_metaclonotypes (specifically on bkgd_cntl_nn2 function) #82

Closed elulu3 closed 1 year ago

elulu3 commented 1 year ago

Hi, I have been following along the find_metaclonotypes function provided in the documentation but found myself stuck on how to use the bkgd_cntl_nn2 function. My antigen-enriched dataset is around 100k rows and so in the initialization of the TCRrep class, I have set compute_distances = FALSE and ran compute_sparse_rect_distances. If I am understanding correctly, this outputs a tr.rw_beta result rather than a tr.pw_beta result. And so here lies my confusion because bkgd_cntl_nn2 seems to require a pw_mat_str input but I don't have a pw_beta result computed. What should I be providing to this parameter ('rw_beta'?)? What exactly is the difference between pw_beta and rw_beta?

elulu3 commented 1 year ago

Received an answer - find_metaclonotypes is not meant to be run on 100k rows. I believe the recommendation was <=15,000 clones.