Annotate clonotypes using immune receptor databases with known condition-associated receptors. Before using this function, you need to download database files first. For more details see the tutorial https://immunarch.com/articles/web_only/v11_db.html.
dbAnnotate(.data, .db, .data.col, .db.col)
.data | The data to process. It can be a data.frame, a data.table, or a list of these objects. Every object must have columns in the immunarch compatible format. immunarch_data_format Competent users may provide advanced data representations: DBI database connections, Apache Spark DataFrame from copy_to or a list of these objects. They are supported with the same limitations as basic objects. Note: each connection must represent a separate repertoire. |
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.db | A data frame or a data table with an immune receptor database. See dbLoad on how to load databases into R. |
.data.col | Character vector. Vector of columns in the input repertoires to use for clonotype search. E.g., `"CDR3.aa"` or `c("CDR3.aa", "V.name")`. |
.db.col | Character vector. Vector of columns in the database to use for clonotype search. The order must match the order of ".data.col". E.g., if ".data.col" is `c("CDR3.aa", "V.name")`, then ".db.col" must have the exact order of columns. i.e., the first column must correspond to CDR3 amino acid sequences, and the second column must correspond to V gene segment names. |
Data frame with input sequences and counts or proportions for each of the input repertoire.