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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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Database lookup not working #36

Closed LBH2021 closed 1 year ago

LBH2021 commented 1 year ago

I am able to successfully load the VDJdb. However, when trying to take the next steps I get the following error:

annotated_VDJ_exact <- VDJ_db_annotate(VDJ = TestVGM,

  • db.list = VDJdb,
  • database.features = 'VDJ_cdr3s_aa',
  • match = 'cdr3.aa',
  • homology = F) MAC system detected Error in VDJ[which(VDJ$Nr_of_VDJ_chains == 1 & VDJ$Nr_of_VJ_chains == : incorrect number of dimensions

If I change the code to:

annotated_VDJ_exact <- VDJ_db_annotate(VDJ = TestVGM[[1]],

  • db.list = VDJdb,
  • database.features = 'VDJ_cdr3s_aa',
  • match = 'cdr3.aa',
  • homology = F) MAC system detected

... I get the above message, but the program never advances beyond this. Any help would be greatly appreciated as I am hoping to use this workflow in my analyses. Thank you!

tudorcotet commented 1 year ago

Hi! Again, sorry for the late reply!

Unfortunately, the current iteration of the VDJ_db_annotate (and the underlying VDJ_antigen_integrate we use for exact/homology matching features based on sequences) is quite slow for really large VGM objects. This might be the reason it is not advancing in your case. I would recommend subsetting your VDJ object to just a few cells and see if it is working/ any errors that might show up!