Identify which single chains were paired

For each sample in the dataset, identify_paired() annotates the alpha and beta pseudobulk data with the number of distinct pairs each chain is a part of in the paired data as well as a TRUE/FALSE column indicating whether the chain is paired with any partners.

Usage

identify_paired(data, verbose = TRUE, by_method = TRUE)

Arguments

data

a TIRTLseq dataset created by load_tirtlseq()

verbose

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

by_method

(optional) whether to get stats for each pairing method

Value

A dataset similar to that created by load_tirtlseq(), but with added columns is_paired and n_paired in the alpha and beta pseudobulk data frames.

is_paired is TRUE if the chain is found in the paired data. n_paired is the number of distinct chains that the particular chain is paired with.

See also

load_tirtlseq()

Other data_processing: TIRTL_process(), 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(), make_tcr_schema(), prep_for_tcrdist(), read_external_bulk(), read_external_paired(), remove_duplicates()

Examples

# example code
# paired = load_tirtlseq("path_to/your_directory", sep = "_", meta_columns = c("cell_type", "timepoint"))
# paired = identify_paired(paired)