check_ontology_translate

make sure ontology names are all translated to ontology ids
while warning, consider manual reannotation

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

check_ontology_translate function

<dl><dt>obj</dt>
<dd>seurat rds object</dd>
<dt>onts</dt>
<dd>ontology ids from translate</dd>
<dt>ont</dt>
<dd>ontologyIndex object</dd>
<dt>anno_col</dt>
<dd>annotation column in obj@meta.data that is translated to onts ids</dd></dl>

Arguments

make sure ontology names are all translated to ontology ids
while warning, consider manual reannotation — check_ontology_translate

<dl>

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


<dt>onts</dt>
<dd>ontology ids from translate</dd>


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


<dt>anno_col</dt>
<dd>annotation column in obj@meta.data that is translated to onts ids</dd>

</dl>

check_ontology_translate: make sure ontology names are all translated to ontology ids while warning, consider manual reannotation

Description

Usage

Value

Arguments