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Returns all of the paired TCRs from all samples in a dataset

get_all_tcrs.Rd

The get_all_tcrs() function aggregates the TCRs from all samples of a dataset and puts them into one table.

Usage

get_all_tcrs(
  data,
  chain = c("paired", "alpha", "beta"),
  remove_duplicates = TRUE
)

Arguments

data

a TIRTLseq dataset created by load_tirtlseq()

chain

the TCR chain, "alpha", "beta", or "paired" (default is paired)

remove_duplicates

only return one TCR pair for TCRs recognized by both the T-SHELL and MAD-HYPE algorithms (default is TRUE).

Value

A dataframe including all of the TCRs in a dataset.

Details

A pair of TCRs is included twice in the TIRTLseq data if it is recognized by both the T-SHELL and MAD-HYPE algorithms. If remove_duplicates is TRUE (default) the function will only return one of these pairs of TCRs.

See also

load_tirtlseq()

Other repertoire_analysis: TCRdist(), TCRdist_cpp(), calculate_diversity(), cluster_tcrs(), get_all_div_metrics(), get_pair_stats(), get_paired_by_read_fraction_range(), summarize_data()

Examples

# example code