Find clonotypes

Identify groups of related cells from allele frequency data. This will cluster the cells based on their allele frequencies, reorder the factor levels for the cluster identities by hierarchical clustering the collapsed (pseudobulk) cluster allele frequencies, and set the variable features for the allele frequency assay to the order of features defined by hierarchical clustering.

FindClonotypes(
  object,
  assay = NULL,
  features = NULL,
  metric = "cosine",
  resolution = 1,
  k = 10,
  algorithm = 3
)

Arguments

object

A Seurat object

assay

Name of assay to use

features

Features to include when constructing neighbor graph

metric

Distance metric to use

resolution

Clustering resolution to use. See FindClusters

k

Passed to k.param argument in FindNeighbors

algorithm

Community detection algorithm to use. See FindClusters

Value

Returns a Seurat object