Add TypoClust cell type annotations to a single-cell object

Adds inferred cell type annotations from a TypoClust object to the metadata of a Seurat or SingleCellExperiment object.

Usage

addTypoData(
  obj,
  typoClust,
  clusters,
  rank_thresh = 1,
  refine = TRUE,
  refine_thresh = 1,
  outNames = NULL
)

Arguments

obj: An object of class Seurat or SingleCellExperiment.
typoClust: An object of class TypoClust, generated using typoClust().
clusters: Character vector; names of metadata columns in obj defining clusters or cell subsets to which cell types will be assigned.
rank_thresh: Integer; the top N ranked cell types to add for each cluster, stored as separate metadata columns.
refine: Logical; whether to refine inferred cell types by traversing deeper levels of the cell type hierarchy.
refine_thresh: Integer; depth of (lexical) hierarchical traversal for refinement. Ignored if refine = FALSE.
outNames: Character vector; names of output metadata columns. If NULL, defaults to paste0(clusters, "_Celltype").

Value

The input object obj with additional metadata columns containing inferred cell type annotations.

Details

Cell type labels are assigned to specified cluster or subset columns and appended as new metadata columns. Multiple ranked cell types can be added, and hierarchical refinement can be applied to obtain more specific cell type annotations.

Examples

if (FALSE) { # \dontrun{
so <- addTypoData(
  obj = so,
  typoClust = tc,
  clusters = "ClustoCell_Clusters"
)
} # }