Signac: FindClonotypes – R documentation

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FindClonotypes

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

Analysis of Single-Cell Chromatin Data

v1.2.1

MIT + file LICENSE

Authors

Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)

Initial release

2021-05-11