cell2go: Get GO ids from cell types

In jvfe/go2cell: Get Cell Types Related to Gene Ontology IDs

Get GO ids from cell types

Description

Return GO identifiers related to gene markers of specific cell types.

Usage

cell2go(celltype_qids)

Arguments

celltype_qids

A character vector of cell type Wikidata IDs

Details

This function takes in a character vector of cell type Q identifiers (QIDs), queries Wikidata (https://www.wikidata.org/) and a local RDF database to return GO IDs related to gene markers of these cell types.

Value

A dataframe of 5 columns: The first two correspond to cell types, that is, their Wikidata Identifier and their name. The two following columns correspond to the Gene Ontology IDs given, and the last column corresponds to the cell type's marker that led to the result.

See Also

https://www.wikidata.org/ for information regarding Wikidata and https://panglaodb.se/index.html for the original database this information was adapted from. For an example of a cell type item in Wikidata, see https://www.wikidata.org/wiki/Q101405098

Examples

# Return GO IDs related to cell type
# 'human smooth muscle cell'
cell2go("Q101404901")
## Not run: 
# IDs should always start with 'Q'
go2cell("101404901")

## End(Not run)

jvfe/go2cell documentation built on Sept. 11, 2023, 4:18 a.m.