ontoMinimal: get the minimal ontology tree of a dataset by reducing...

In scOntoMatch: Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'

get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[["cell_ontology_base"]] storing the reduced ontology annotation

Description

get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[["cell_ontology_base"]] storing the reduced ontology annotation

Usage

ontoMinimal(obj, ont, anno_col, onto_id_col)

Arguments

obj	the seurat object
ont	ontologyIndex object
anno_col	the cell ontology text annotation column name
onto_id_col	if also have ontology id column for direct mapping

Value

an seurat object with meta.data[["cell_ontology_base"]]

Examples

## Not run: 
ontoMinimal(obj = seurat_obj, ont = ont, anno_col = 'ontology_name', onto_id_col = 'ontology_id')

## End(Not run)

scOntoMatch documentation built on Nov. 2, 2023, 5:20 p.m.