Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'

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Documentation for package ‘scOntoMatch’ version 0.1.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

check_ontology_translate	make sure ontology names are all translated to ontology ids while warning, consider manual reannotation
fill_query	Get a names list of ontology and id by id
getOntologyId	Get a names list of ontology and id by name
getOntologyName	Get a names list of ontology and id by id
getOntoMapping	match ontology terms by direct mapping and mapping descendants to ancestors
getOntoMinimal	match descendant terms to ancestor terms within a dataset
getOntoMultiMapping	Match descendants to ancestors in multiple ontology id lists
getSeuratRds	read in seurat object .rds files as a named list of seurat object
ontoMinimal	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
ontoMultiMatch	Core function of scOntoMatch Match the ontology annotation of multiple seurat objects
ontoMultiMinimal	get the minimal ontology tree of a list of seurat objects by reducing descendant terms to ancestor terms return a named list of seurat objects with meta.data[["cell_ontology_base"]] storing the reduced ontology annotation
ontoTranslate	translate named list of obj_list to named list of cell ontology ids per obj
plotMatchedOntoTree	Plot a ontology tree with matched ontology from ontoMatch
plotOntoTree	Plot a tree representation of ontology terms