Get cell types from GO ids
go2cell.RdReturn cell type information for specific Gene Ontology identifiers
Arguments
- go_ids
A character vector of Gene Ontology identifiers.
- species
A character of a species, can either be Homo sapiens (default) or Mus musculus.
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.
Details
This function takes in a character vector of Gene Ontology (GO) identifiers, queries Wikidata (https://www.wikidata.org/) for genes related to said identifiers, and crosses this data with a local RDF database of cell type-marker correspondence, returning, at last, a dataframe of cell type information related to the given GO identifiers.
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.
Examples
# Return cell types related to 'muscle contraction' and 'metabolism'
go2cell(c("GO:0006936", "GO:0008152"))
#> Rows: 354 Columns: 5
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (5): cell_type, cell_typeLabel, go_ids, go_termLabel, geneLabel
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
# Return cell types related to 'response to zinc ion'
go2cell("GO:0010043")
#> Rows: 79 Columns: 5
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr (5): cell_type, cell_typeLabel, go_ids, go_termLabel, geneLabel
#>
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
if (FALSE) {
# IDs should use ':' not '_'
go2cell("GO_0010043")
}