Run data processing functions on a TIRTLseqDataSet object

This function runs annotation and data cleaning functions on a TIRTLseqDataSet object. Specifically, it calls the functions add_single_chain_data(), identify_paired(), identify_non_functional_seqs(), and (optionally) clean_pairs().

Usage

TIRTL_process(...)

process_TIRTLseq(data, clean = FALSE, remove_nonfunctional = FALSE)

Arguments

data

a TIRTLseqDataSet object

clean

(optional) a TRUE/FALSE value, whether or not to "clean" the paired data by removing excess pairs for individual alpha and beta chains (default is FALSE).

remove_nonfunctional

whether to remove non-functional TCR chains (default is FALSE)

Value

a TIRTLseqDataSet object with annotated and (optionally) cleaned data

See also

Other data_processing: add_single_chain_data(), clean_pairs(), combine_bulk_and_paired_data(), filter_duplicate_tcrs(), filter_mait(), 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()