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

Unequal granularity of cell type annotation makes it difficult to compare scRNA-seq datasets at scale. Leveraging the ontology system for defining cell type hierarchy, 'scOntoMatch' aims to align cell type annotations to make them comparable across studies. The alignment involves two core steps: first is to trim the cell type tree within each dataset so each cell type does not have descendants, and then map cell type labels cross-studies by direct matching and mapping descendants to ancestors. Various functions for plotting cell type trees and manipulating ontology terms are also provided. In the Single Cell Expression Atlas hosted at EBI, a compendium of datasets with curated ontology labels are great inputs to this package.

Yuyao Song

scOntoMatch

Aligning Ontology Annotation Across Single Cell Datasets with
'scOntoMatch'

Irene Papatheodorou

ontoMinimal function

<dl><dt>obj</dt>
<dd>the seurat object</dd>
<dt>ont</dt>
<dd>ontologyIndex object</dd>
<dt>anno_col</dt>
<dd>the cell ontology text annotation column name</dd>
<dt>onto_id_col</dt>
<dd>if also have ontology id column for direct mapping</dd></dl>

Arguments

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 — ontoMinimal

<dl>

<dt>obj</dt>
<dd>the seurat object</dd>


<dt>ont</dt>
<dd>ontologyIndex object</dd>


<dt>anno_col</dt>
<dd>the cell ontology text annotation column name</dd>


<dt>onto_id_col</dt>
<dd>if also have ontology id column for direct mapping</dd>

</dl>

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

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

Description

Usage

Value

Arguments

Examples