error

[LaCie1981]

Your question

At first, thanks for this really useful tools for neophytes. I have previously used Immunarch9.0 and try now to adapt my analysis to the new version.
However I now face a error when creating the ImmunData object.

idata <- read_repertoires(path = inp_files, schema = schema, metadata = md_table, repertoire_schema = "Status")

It gives the following error message:

"── Aggregating the data to receptors
Error in rlang::sym():
! Can't convert NULL to a symbol.
Run rlang::last_trace() to see where the error occurred."

As I am using a raw files with a specific format, I understand my files would require a formatting to get an AIRR-C compliant file.... I was used to change the columns order to adapt to Immunarch9.0 but I am completely naive about AIRR-C.

Here is an example of my files:
SLa0002a-2024-00844_TCRa_Immunarch.tsv

Thanks in advance,

[LaCie1981]

I finally found a solution for the error I faced (basic error from my side).
However I have now a technical question:
My "receptor" is defined as :
schema <- make_receptor_schema(features = c("CDR3_aaseq", "TRAV", "TRAJ"))

But, some clones are out of frame and give no CDR3_aaseq despite a TRAV and a TRAJ annotation.
How will this clones considered? As a receptor? Or will they leave untreated?

Thanks for your answer.