Match TCRs to a literature database

Wrapper around find_significant_tcrdist_matches that loads a default or custom database file.

Usage

match_tcrs_to_db(
  tcr_df,
  organism,
  db_tcrs_tsvfile = NULL,
  adjusted_pvalue_threshold = 1,
  background_tcrs_df = NULL,
  num_random_samples = 50000L
)

Arguments

tcr_df

A data.frame with columns va, ja, cdr3a, cdr3a_nucseq, vb, jb, cdr3b, cdr3b_nucseq.

organism

Character string.

db_tcrs_tsvfile

Path to a TSV file with database TCRs. If NULL, uses the built-in new_paired_tcr_db_for_matching_nr.tsv (human only).

adjusted_pvalue_threshold

Numeric. Default 1.0.

background_tcrs_df

Optional background data.frame.

num_random_samples

Integer. Default 50000L.

Value

A data.frame of significant matches (see find_significant_tcrdist_matches).

See also

find_significant_tcrdist_matches, strict_single_chain_match_tcrs_to_db

Examples

if (FALSE) { # \dontrun{
results <- match_tcrs_to_db(tcr_df, organism = "human")
results[results$pvalue_adj < 0.05, ]
} # }