# Aligning Ontology Annotation Across Single Cell Datasets with 'scOntoMatch'

## Documentation for package ‘scOntoMatch’ version 0.1.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package README

## 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