Remove MAIT (Mucosal-Associated Invariant T cells) TCRs

This function uses a heuristic to remove TCRs associated with MAIT cells, which may not be desired for some applications. For example, when creating a network of related TCRs with TCRdist, these TCRs often form a very highly dense sub-network that inflates output file size.

Usage

filter_mait(df, verbose = TRUE)

Arguments

df

data frame with paired TCRs

verbose

whether to print number of MAIT TCRs removed

Value

A data frame with MAIT TCRs removed

Details

We use a heiristic where we remove TCRs with V-alpha TRAV1-2 and either J-alpha segment TRAJ33, TRAJ12, or TRAJ20 (see Garner et al. 2023 - https://www.nature.com/articles/s41590-023-01575-1).

See also

Other data_processing: TIRTL_process(), add_single_chain_data(), clean_pairs(), combine_bulk_and_paired_data(), filter_duplicate_tcrs(), filter_nonfunctional_TCRs(), filter_short_cdr3s(), filter_v_alleles(), identify_non_functional_seqs(), identify_paired(), make_tcr_schema(), prep_for_tcrdist(), read_external_bulk(), read_external_paired(), remove_duplicates()