calc_similarity: Calculate repertoire similarity between clusters

In friedue/SCEdjvdj: Single-cell VDJ Tools for SCE objects

Description

Calculate repertoire similarity between clusters

Usage

calc_similarity(
  SCE_in,
  clonotype_col = "cdr3_nt",
  cluster_col,
  method = abdiv::jaccard,
  prefix = NULL,
  return_SCE = TRUE
)

Arguments

SCE_in	Seurat object
clonotype_col	meta.data column containing clonotype IDs to use for calculating overlap
cluster_col	meta.data column containing cluster IDs to use for calculating overlap
method	Method to use for calculating similarity between clusters
prefix	Prefix to add to new meta.data columns
return_SCE	Return a Seurat object. If set to FALSE, a matrix is returned

Value

Seurat object with similarity index added to meta.data

Author(s)

djvdj authors

friedue/SCEdjvdj documentation built on April 21, 2021, 7:54 a.m.