dbAnnotate questions

[scas224]

Hi! I am following the tutorial for annotating clonotypes using immune receptor databases, and I had a few questions.

First, if I'm only working with data for one sample, am I able to annotate the clonotypes in that sample? It appears that this is not possible because when I try to run dbAnnotate on the data, it prompts this error: Error in trackClonotypes(.data, .db %>% select(.data.col), .norm = FALSE) : Error: please pass a list with 2 or more immune repertoires to track clonotypes

Also, how would you recommend adding the information from the database to our data? For example, if we use dbAnnotate to match up CDR3 amino acid sequences from our data to sequences from the database, how could we attach the MHC and epitope information to the clonotype it matched to?

Thanks!

[MVolobueva]

Hi, @scas224 !

You have asked really good questions!:)

First, if I'm only working with data for one sample, am I able to annotate the clonotypes in that sample?

Fisrt of all, I have no idea about error in trackClonotypes. trackClonotypes and dbAnnotate are two different and separate functions. Could you please provide an example of your data that I managed to reproduce that error.

Also, how would you recommend adding the information from the database to our data?

Currently I recommend using standart R finction like merge and writing something like this:

merge(your_data, database_data, by = 'cdr3')

Аdding this feature is an excellent idea to improve Immunarch. We will think about it!

Thank you again for contacting us!

Enjoy your week, Maria Samokhina