Identify TCRs that contain non-functional CDR3 sequences, i.e. those that contain stop codons (*) or frame shifts (_)

identify_non_functional_seqs() identifies CDR3 nucleotide sequences in the data that contain errors, either stop codons (*) or frame shifts (_) that would indicate a non-functional chain.

Usage

identify_non_functional_seqs(df)

Arguments

df

a dataframe of TIRTLseq data, either paired or single-chain pseudobulk for one sample

Value

A dataframe with added columns that identify whether the CDR3 alpha and beta nucleotide sequences contain any stop codons (*) or frame shifts (_) that would indicate a non-functional chain.

If column is_functional is TRUE if neither chain has a stop codon or a frame shift. The columns has_stop_codon and has_frameshift are similar, but specific to each kind of coding error. Other columns identify if the alpha chain or beta chain has a stop codon or frameshift, and if it is functional.

See also

TCRdist(), plot_num_partners()

Other data_processing: TIRTL_process(), add_single_chain_data(), clean_pairs(), identify_paired(), prep_for_tcrdist(), remove_duplicates()

Examples

# example code