FindClonotypes function

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

Returns

Returns a Seurat object