combineTCR: Combining the list of T cell receptor contigs into clones

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Combining the list of T cell receptor contigs into clones

Description

This function consolidates a list of TCR sequencing results to the level of the individual cell barcodes. Using the samples and ID parameters, the function will add the strings as prefixes to prevent issues with repeated barcodes. The resulting new barcodes will need to match the Seurat or SCE object in order to use, combineExpression. Several levels of filtering exist - removeNA, removeMulti, or filterMulti are parameters that control how the function deals with barcodes with multiple chains recovered.

Usage

combineTCR(
  input.data,
  samples = NULL,
  ID = NULL,
  removeNA = FALSE,
  removeMulti = FALSE,
  filterMulti = FALSE,
  filterNonproductive = TRUE
)

Arguments

input.data	List of filtered contig annotations or outputs from loadContigs.
samples	The labels of samples (recommended).
ID	The additional sample labeling (optional).
removeNA	This will remove any chain without values.
removeMulti	This will remove barcodes with greater than 2 chains.
filterMulti	This option will allow for the selection of the 2 corresponding chains with the highest expression for a single barcode.
filterNonproductive	This option will allow for the removal of nonproductive chains if the variable exists in the contig data. Default is set to TRUE to remove nonproductive contigs.

Value

List of clones for individual cell barcodes

Examples

combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

ncborcherding/scRepertoire documentation built on May 8, 2024, 6:28 a.m.