pkgdown/extra.css Skip to contents

Read and process bulk single-chain TCR-seq data

read_external_bulk.Rd

[Experimental] This function reads and processes bulk single-chain TCR-sequencing data from a non-TIRTLseq assay. Currently, only MiXCR format is supported.

Usage

read_external_bulk(path, format = "MiXCR")

Arguments

path

the path to the data file

format

the data format. Currently only "MiXCR" is supported.

Value

A list containing the following slots:

  • df - a data frame with a few columns modified and renamed

  • df_raw - the original data, un-modified

Details

Supported data types:

  • "MiXCR" - "<sample_name>_TRA.tsv" and "<sample_name>_TRB.tsv"

See also

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(), identify_paired(), make_tcr_schema(), prep_for_tcrdist(), read_external_paired(), remove_duplicates()