Cloning fails on single-cell TCR data

Issue #18 resolved
Jason Vander Heiden created an issue

Looks like everything is hardcode to IGH, IGL and IGK. The code should work for TCR data as well (TRB, TRD, TRA, TRG).

The problem is also present in the single-cell modes for alakazam::groupGenes and shazam::distToNearest. It may not be essential to fix this in distToNearest, but I also don’t see a reason not to fix it because you may want to use distToNearest on TCR data for purposes other than clonal clustering.

The only_igh argument should probably be changed accordingly, so as not to be confusing. only_heavy would be better - still wrong, but less wrong.

Comments (2)

  1. Log in to comment