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Prepare paired TCRs for TCRdist calculation

prep_for_tcrdist.Rd

[Experimental] This function prepares a paired TCR data frame for running TCRdist, adding alleles to V-segments (i.e. "*01") if they are missing and removing TCRs with unrecognized V-segments or non-functional CDR3 sequences.

Usage

prep_for_tcrdist(
  df,
  params = NULL,
  remove_duplicate_tcrs = FALSE,
  remove_MAIT = TRUE,
  verbose = TRUE
)

Arguments

df

a data frame with one TCR per row. It must have the columns "va", "vb", "cdr3a", and "cdr3b"

params

(optional) a data frame with permissible amino acids and V-segments. By default, the params data frame is used.

remove_duplicate_tcrs

(optional) whether or not to remove duplicate TCRs (default is FALSE, do not remove duplicates).

remove_MAIT

(optional) whether or not to remove MAIT cells from the data frame (default is TRUE).

verbose

(optional) whether to print progress of the function (default is TRUE).

Value

Returns a paired TCR data frame that is compatible with TCRdist python scripts.

See also

Other data_processing: TIRTL_process(), add_single_chain_data(), clean_pairs(), filter_duplicate_tcrs(), filter_mait(), filter_nonfunctional_TCRs(), filter_short_cdr3s(), filter_v_alleles(), identify_non_functional_seqs(), identify_paired(), remove_duplicates()