Given a gene, what phenotypes are associated with it.
bioentity_phenotypes_assoc_w_gene(gene, rows = 100)
| gene | A valid monarch initiative gene id. |
|---|---|
| rows | Number of rows of results to fetch. |
A list of (tibble of phenotype information, monarch_api S3 class).
https://api.monarchinitiative.org/api/bioentity/gene/NCBIGene
gene <- "NCBIGene:8314" bioentity_phenotypes_assoc_w_gene(gene)#> $phenotypes #> # A tibble: 20 x 10 #> subject.taxon subject.id subject relation object object.id object.taxon #> * <chr> <chr> <chr> <chr> <chr> <chr> <lgl> #> 1 Homo sapiens HGNC:950 BAP1 has phen… Metamorph… HP:00125… NA #> 2 Homo sapiens HGNC:950 BAP1 has phen… Zonular c… HP:00109… NA #> 3 Homo sapiens HGNC:950 BAP1 has phen… Intraocul… HP:00077… NA #> 4 Homo sapiens HGNC:950 BAP1 has phen… Mydriasis HP:00114… NA #> 5 Homo sapiens HGNC:950 BAP1 has phen… Choroidal… HP:00120… NA #> 6 Homo sapiens HGNC:950 BAP1 has phen… Ocular pa… HP:02000… NA #> 7 Homo sapiens HGNC:950 BAP1 has phen… Lung aden… HP:00300… NA #> 8 Homo sapiens HGNC:950 BAP1 has phen… Vitreous … HP:00079… NA #> 9 Homo sapiens HGNC:950 BAP1 has phen… Abnormal … HP:00308… NA #> 10 Homo sapiens HGNC:950 BAP1 has phen… Photopsia HP:00307… NA #> 11 Homo sapiens HGNC:950 BAP1 has phen… Iris mela… HP:00115… NA #> 12 Homo sapiens HGNC:950 BAP1 has phen… Meningioma HP:00028… NA #> 13 Homo sapiens HGNC:950 BAP1 has phen… Inferior … HP:00084… NA #> 14 Homo sapiens HGNC:950 BAP1 has phen… Increased… HP:00079… NA #> 15 Homo sapiens HGNC:950 BAP1 has phen… Abnormali… HP:00005… NA #> 16 Homo sapiens HGNC:950 BAP1 has phen… Retinal d… HP:00005… NA #> 17 Homo sapiens HGNC:950 BAP1 has phen… Cutaneous… HP:00120… NA #> 18 Homo sapiens HGNC:950 BAP1 has phen… Visual lo… HP:00005… NA #> 19 Homo sapiens HGNC:950 BAP1 has phen… Ciliary b… HP:00120… NA #> 20 Homo sapiens HGNC:950 BAP1 has phen… Inflammat… HP:01005… NA #> # ... with 3 more variables: evidence <fct>, publications <fct>, #> # provided_by <fct> #> #> $response #> <monarch https://api.monarchinitiative.org/api/bioentity/gene/NCBIGene%3A8314/phenotypes/?rows=100&fetch_objects=true&format=json> #> <Showing parsed R objects from json response. 2 level(s) deep> #> List of 7 #> $ compact_associations: NULL #> $ associations :'data.frame': 20 obs. of 14 variables: #> ..$ provided_by :List of 20 #> ..$ relation :'data.frame': 20 obs. of 2 variables: #> ..$ object_extensions : logi [1:20] NA NA NA NA NA NA ... #> ..$ publications :List of 20 #> ..$ object :'data.frame': 20 obs. of 3 variables: #> ..$ negated : logi [1:20] FALSE FALSE FALSE FALSE FALSE FALSE ... #> ..$ slim : logi [1:20] NA NA NA NA NA NA ... #> ..$ subject_extensions: logi [1:20] NA NA NA NA NA NA ... #> ..$ type : logi [1:20] NA NA NA NA NA NA ... #> ..$ qualifiers : logi [1:20] NA NA NA NA NA NA ... #> ..$ evidence_graph :'data.frame': 20 obs. of 2 variables: #> ..$ evidence_types : logi [1:20] NA NA NA NA NA NA ... #> ..$ id : chr [1:20] "45389be9-cfc5-4d4a-bb39-b30268ca80aa" "1319a2e1-61c2-4635-bd13-a87573deec4c" "ed49f5c7-5646-4716-a017-5cf826cdf1ca" "46e48687-f429-4da4-8dc9-d07fedd8b249" ... #> ..$ subject :'data.frame': 20 obs. of 3 variables: #> $ objects : chr [1:20] "HP:0000539" "HP:0000541" "HP:0000572" "HP:0002858" ... #> $ highlighting : NULL #> $ numFound : NULL #> $ facet_counts :List of 2 #> ..$ subject_taxon_label:List of 1 #> ..$ object_closure :List of 25 #> $ docs : NULL #>