dbAnnotate problems

[giuliabriss]

❓ Questions and Help

Hello,
I am reaching out to inquire about the dbAnnotate function.
First of all, I'd like to tell you that I am really new into R programming.
The goal of my analysis is to understand if a list of CDR3 sequences, selected from a cohort of patients, are present or not in a set of healthy donors. For testing purpose, I've dowloaded immune repertoire data of 10 healthy donors from the immuneACCESS.
This is the code I run:

library(immunarch)

#Load the list of CDR3 sequences, which were selected from patients
local_db <- read_csv("Unknonw-sequences.csv")
local_db

#A tibble: 1,733 × 6
#ID amino_acid pre post meso ratio
#
#1 80-86-Meso110A CASSPGTGVYGYTF 0.0000180 0.0000987 5.49 0.00000722
#2 80-86-Meso110A CASSLVPDTQYF 0.0000180 0.0000987 5.49 0.0000108

#load immune repertoire data of 10 healthy donors downloaded from immunoseq analyzer
healthy <- repLoad("healthy_donors")
results <- dbAnnotate(healthy$data, local_db, "CDR3.aa", "amino_acid")
write_csv(results, "results.csv")

The results is similar to the expected one. However, when I tried to manually cross-check a few sequences from my local_db against the healthy$data to see if the count match and are being annotated correctly, I found few errors (for instance: dbAnnotate counts the selected sequences 10 times in the healthy donors X, when it is present 4 times).

Do you have any suggestion? What am I doing wrong?

Thanks a lot!