HPO phenotypes Monarch associates with a gene — monarch_gene

Keyed on the HGNC id, which mygene_gene() returns as hgnc. The rows come back in the shape monarch_parse_associations() describes, so the phenotype term is object and its label is object_label.

Usage

monarch_gene_phenotypes(hgnc, limit = 50, ...)

Arguments

hgnc: An HGNC id, bare or prefixed. See monarch_hgnc_id().
limit: Maximum associations to return.
...: Passed to biohttp::get_json(), for example throttle.

Value

A biohttp envelope whose data is a list of associations (the tibble) and total.

References

Putman et al. (2024). The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Research 52(D1), D938-D949. doi:10.1093/nar/gkad1082

Service documentation: https://monarchinitiative.org/

Examples

# \donttest{
biohttp::body_or_null(monarch_gene_phenotypes("11998"))$associations
#> # A tibble: 48 × 10
#>    subject    subject_label subject_category predicate       object object_label
#>    <chr>      <chr>         <chr>            <chr>           <chr>  <chr>       
#>  1 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Anemia      
#>  2 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Decreased c…
#>  3 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Erythroid h…
#>  4 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Global deve…
#>  5 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Growth delay
#>  6 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Hypogonadism
#>  7 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Intellectua…
#>  8 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Microcephaly
#>  9 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Pure red ce…
#> 10 HGNC:11998 TP53          biolink:Gene     biolink:has_ph… HP:00… Reticular h…
#> # ℹ 38 more rows
#> # ℹ 4 more variables: object_category <chr>, primary_knowledge_source <chr>,
#> #   knowledge_level <chr>, publications <list>
# }