regarding 'find.clonotype'

[joonlee3]

Hi Vadim,

I have a question about a tcR function 'find.clonotype'. I am reading through tcR vignette. One of the examples is to show how to search for a target CDR3 sequence. As shown in the vignette, if I run the command lines,

cmv.imm.hamm.v <- find.clonotypes(twb[1:3], cmv, 'hamm', 'Rank',

•                              .target.col = c('CDR3.amino.acid.sequence', 'V.gene'), .verbose = F)
  

  head(cmv.imm.hamm.v)

then we get the following output
CDR3.amino.acid.sequence V.gene Rank.Subj.A Rank.Subj.B Rank.Subj.C
CASSALGGAGTGELFF CASSALGGAGTGELFF TRBV4-1 NA NA NA
CASSLIGVSSYNEQFF CASSLIGVSSYNEQFF TRBV4-1 NA NA NA
CASSLTGNTEAFF CASSLTGNTEAFF TRBV4-1 NA NA NA
CASSSANYGYTF CASSSANYGYTF TRBV4-1 NA NA NA
CSVGRAQNEQFF CSVGRAQNEQFF TRBV4-1 NA NA NA

I thought that information from the column "Rank" (which is generated by using set.rank) would be shown in those columns but those three columns are just 'NA'. Would you please explain this? Thanks a lot.

Best,
Joon

[vadimnazarov]

Hi Joon,

it means that no such clonotypes has been found in the data. Thank you for pointing to this examples, they are really not very good cases for showing the functionally of find.clonotypes, so I think I would change them.

[vadimnazarov]

Hi, tcR package is no longer supported and current issues will not be fixed. A new package is available that is designed to replace tcR called immunarch. We have solved most of the problems tcR package had and improved the overall pipeline, providing functions for painless repertoire file parsing and publication-ready plot making.

The mission of the immunarch is to make immune repertoire data analysis as easy and possible—even with R. Please feel free to check it here: https://immunarch.com/

If you have any suggestions, bugs, improvements, etc. -- please write us or create an issue in https://github.com/immunomind/immunarch/issues

Thank you! Sincerely,
immunarch dev team and Vadim I. Nazarov, lead developer