ontoTranslate

translate named list of obj_list to named list of cell ontology ids per obj

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

ontoTranslate function

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

Arguments

translate named list of obj_list to named list of cell ontology ids per obj — ontoTranslate

<dl>

<dt>obj_list</dt>
<dd>a named list of seurat object</dd>


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


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


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

</dl>

ontoTranslate: translate named list of obj_list to named list of cell ontology ids per obj

Description

Usage

Value

Arguments

Examples