FindClonotypes: Find clonotypes

In Signac: Analysis of Single-Cell Chromatin Data

Find clonotypes

Description

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.

Usage

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

Signac documentation built on Sept. 11, 2024, 9:30 p.m.