Strict CDR3 sequence matching against a database — strict_single_chain_match_tcrs_to_db • tcrdistR

Finds database entries where the CDR3alpha or CDR3beta amino acid sequence exactly matches a query TCR.

Usage

strict_single_chain_match_tcrs_to_db(tcr_df, organism, db_tcrs_tsvfile = NULL)

Arguments

tcr_df: A data.frame with columns cdr3a and cdr3b.
organism: Character string (e.g. "human", "mouse").
db_tcrs_tsvfile: Path to a TSV file. If NULL, uses the built-in organism-specific single-chain database.

Value

A list with elements alpha_matches and beta_matches, each a data.frame of matching database rows.

See also

match_tcrs_to_db, find_significant_tcrdist_matches

Examples

if (FALSE) { # \dontrun{
hits <- strict_single_chain_match_tcrs_to_db(tcr_df, "human")
hits$alpha_matches
hits$beta_matches
} # }