Given a gene, what pathways are associated with it.
bioentity_pathways_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 pathways information, monarch_api S3 class).
https://api.monarchinitiative.org/api/bioentity/gene/HGNC
gene <- "NCBIGene:8314" bioentity_pathways_assoc_w_gene(gene)#> $pathways #> # A tibble: 8 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 involved… UCH protei… REACT:R-… NA #> 2 Homo sapiens HGNC:950 BAP1 involved… Post-trans… REACT:R-… NA #> 3 Homo sapiens HGNC:950 BAP1 involved… Recruitmen… REACT:R-… NA #> 4 Homo sapiens HGNC:950 BAP1 involved… Deubiquiti… REACT:R-… NA #> 5 Homo sapiens HGNC:950 BAP1 involved… Metabolism… REACT:R-… NA #> 6 Homo sapiens HGNC:950 BAP1 involved… DNA Repair REACT:R-… NA #> 7 Homo sapiens HGNC:950 BAP1 involved… DNA Double… REACT:R-… NA #> 8 Homo sapiens HGNC:950 BAP1 involved… DNA Double… REACT:R-… NA #> # ... with 3 more variables: evidence <fct>, publications <fct>, #> # provided_by <fct> #> #> $response #> <monarch https://api.monarchinitiative.org/api/bioentity/gene/NCBIGene%3A8314/pathways/?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': 8 obs. of 14 variables: #> ..$ provided_by :List of 8 #> ..$ relation :'data.frame': 8 obs. of 2 variables: #> ..$ object_extensions : logi [1:8] NA NA NA NA NA NA ... #> ..$ publications : logi [1:8] NA NA NA NA NA NA ... #> ..$ object :'data.frame': 8 obs. of 3 variables: #> ..$ negated : logi [1:8] FALSE FALSE FALSE FALSE FALSE FALSE ... #> ..$ slim : logi [1:8] NA NA NA NA NA NA ... #> ..$ subject_extensions: logi [1:8] NA NA NA NA NA NA ... #> ..$ type : logi [1:8] NA NA NA NA NA NA ... #> ..$ qualifiers : logi [1:8] NA NA NA NA NA NA ... #> ..$ evidence_graph :'data.frame': 8 obs. of 2 variables: #> ..$ evidence_types : logi [1:8] NA NA NA NA NA NA ... #> ..$ id : chr [1:8] "438a3246-26e5-4fc2-9972-faa602ce67c2" "55287580-d39c-4bbe-af41-288d836420a5" "860918db-088d-49b1-9a65-d647e5c9b851" "d8aba127-3175-4f1c-81f1-227753dc7611" ... #> ..$ subject :'data.frame': 8 obs. of 3 variables: #> $ objects : chr [1:8] "REACT:R-HSA-392499" "REACT:R-HSA-5688426" "REACT:R-HSA-5689603" "REACT:R-HSA-5693532" ... #> $ highlighting : NULL #> $ numFound : NULL #> $ facet_counts :List of 2 #> ..$ subject_taxon_label:List of 1 #> ..$ object_closure :List of 19 #> $ docs : NULL #>