Remove TCRs with nonfunctional CDR3 amino acid sequences

This function removes TCR pairs where the CDR3-alpha or beta segment does not make a functional protein, i.e. amino acid sequence contains a stop codon (*) or a frameshift (_).

Usage

filter_nonfunctional_TCRs(data, verbose = TRUE)

Arguments

data

a TIRTLseqDataSet object

verbose

whether to print number of TCRs removed

Value

Returns a TIRTLseqDataSet object with nonfunctional TCRs removed.

See also

Other data_processing: clean_pairs(), combine_bulk_and_paired_data(), filter_duplicate_tcrs(), filter_mait(), filter_short_cdr3s(), filter_v_alleles(), make_tcr_schema(), prep_for_tcrdist(), remove_duplicates()