Process single-cell TIRTL-seq data

This function reads a directory of MiXCR output files from single-cell TIRTL-seq and outputs a data frame with a single TCR for each well.

Usage

process_scTIRTLseq(
  folder,
  min_read_fraction = 0.1,
  min_read_count = 15,
  require_functional = TRUE
)

Arguments

folder

the path of the folder with .tsv (or .tsv.gz) output files from MiXCR

min_read_fraction

the minimum read fraction required to select a chain for a well

min_read_count

the minimum read count required to select a chain for a well

require_functional

whether to require a functional chain (i.e. without frameshift or stop codons in the CDR3 region)

Value

A data frame with one TCR pair selected per well.

See also

Other single-cell: plot_scTIRTLseq_plate()