annotate_merge_by_cluster: Merge annotation by cluster

In Terkild/scutility: Utility Functions For Multi-modal Single-cell Analysis

Merge annotation by cluster

Description

Merges individual cell annotations by cluster using majority rule (the entire cluster is annotated as the individual annotation represented by most cells within the cluster)

Usage

annotate_merge_by_cluster(
  annotation,
  cluster,
  threshold = "max",
  collapse = "/",
  exclude = c()
)

Arguments

annotation	vector of individual cell annotations (i.e. from SingleR) (one value for each cell)
cluster	vector of cluster assignments (one value for each cell)
threshold	Frequency threshold to be included in new cluster name (use 'max' to only include a single annotation)
collapse	If frequency is not 'max', the annotations that fullfil the threshold are separated by this character
exclude	Vector of annotations that should not be merged, but kept as is (i.e. gdT cells defined by their TCR)

Value

vector of cluster annotations

Terkild/scutility documentation built on Jan. 16, 2025, 5:28 p.m.