quantContig {scRepertoire} | R Documentation

## Quantify the unique clonotypes in the filtered contigs.

### Description

This function takes the output from combineTCR(), combineBCR(), or expression2List() and quantifies unique clonotypes. The unique clonotypes can be either reported as a raw output or scaled to the total number of clonotypes recovered using the scale parameter. Multiple sequencing runs can be group together using the group parameter. If a matrix output for the data is preferred, set exportTable = TRUE.

### Usage

    quantContig(
      df,
      cloneCall = "gene+nt",
      scale = FALSE,
      group = NULL,
      exportTable = FALSE
    )

### Arguments

`df` | The product of combineTCR() combineBCR() or expression2List().
`cloneCall` | How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt).
`scale` | Converts the graphs into percentage of unique clonotypes.
`group` | The column header used for grouping.
`exportTable` | Returns the data frame used for forming the graph

### Value

ggplot of the total or relative unique clonotypes

### Examples

    #Making combined contig data
    x <- contig_list
    combined <- combineTCR(x, rep(c("PX", "PY", "PZ"), each=2),
    rep(c("P", "T"), 3), cells ="T-AB")
    quantContig(combined, cloneCall="gene+nt", scale = TRUE)

[Package scRepertoire version 1.4.0 Index]