quantContig: Quantify the unique clonotypes in the filtered contigs.

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

Description

This function takes the output from combineTCR(), combineBCR(), or e xpression2List() 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)

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