combineTCR: Combining the list of T Cell Receptor contigs

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

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, @seealso combineExpression. Several levels of filtering exist - remove or filterMulti are parameters that control how the function deals with barcodes with multiple chains recovered.

Usage

combineTCR(
  df,
  samples = NULL,
  ID = NULL,
  cells = c("T-AB", "T-GD"),
  removeNA = FALSE,
  removeMulti = FALSE,
  filterMulti = FALSE
)

Arguments

df	List of filtered contig annotations from 10x Genomics.
samples	The labels of samples.
ID	The additional sample labeling option.
cells	The type of T cell - T cell-AB or T cell-GD
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.

Value

List of clonotypes for individual cell barcodes

Examples

combineTCR(contig_list, rep(c("PX", "PY", "PZ"), each=2), 
rep(c("P", "T"), 3), cells ="T-AB")

scRepertoire documentation built on Nov. 8, 2020, 7 p.m.