clonalOverlap: Examining the clonal overlap between groups or samples

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

Description

This functions allows for the caclulation and visualizations of the overlap coefficient or morisita index for clonotypes using the product of combineTCR(), combineBCR() or expression2list(). The overlap coefficient is calculated using the intersection of clonotypes divided by the length of the smallest componenet. Morisita index is estimating the dispersion of a population, more information can be found [here](https://en.wikipedia.org/wiki/Morisita If a matrix output for the data is preferred, set exportTable = TRUE.

Usage

clonalOverlap(
  df,
  cloneCall = c("gene", "nt", "aa", "gene+nt"),
  method = c("overlap", "morisita"),
  exportTable = FALSE
)

Arguments

df	The product of combineTCR(), combineBCR(), or expression2List().
cloneCall	How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt) or CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt).
method	The method to calculate the overlap, either the overlap coefficient or morisita index.
exportTable	Exports a table of the data into the global environment in addition to the visualization

Value

ggplot of the clonotypic overlap between elements of a list

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")

clonalOverlap(combined, cloneCall = "gene", method = "overlap")

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