combineTCR {scRepertoire} | R Documentation

## Combining the list of T Cell Receptor contigs

### 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")

[Package scRepertoire version 1.0.0 Index]