Replicates info in view: https://api.monarchinitiative.org/api/#!/bioentity/get_gene_homologs
bioentity_homologs(gene, homolog_taxon = NULL, rows = 100)
| gene | A valid monarch initiative gene id. |
|---|---|
| homolog_taxon | A taxon for the target organism. |
| rows | Number of rows of results to fetch. Taxon takes the form NCBITaxon:id. (human: NCBITaxon:9606) |
A list of (tibble of homolog information, monarch_api S3 class).
mimics calls like these
https://api.monarchinitiative.org/api/bioentity/gene/NCBIGene https://api.monarchinitiative.org/api/bioentity/gene/HGNC
gene <-"NCBIGene:8314" bioentity_homologs(gene)#> $homologs #> # A tibble: 17 x 10 #> subject.taxon subject.id subject relation object object.id object.taxon #> * <chr> <chr> <chr> <chr> <chr> <chr> <chr> #> 1 Homo sapiens HGNC:950 BAP1 in paralog… UCHL5 HGNC:19678 Homo sapiens #> 2 Homo sapiens HGNC:950 BAP1 in paralog… UCHL3 HGNC:12515 Homo sapiens #> 3 Homo sapiens HGNC:950 BAP1 in 1 to 1 … BAP1 NCBIGene:… Equus caball… #> 4 Homo sapiens HGNC:950 BAP1 in 1 to 1 … Bap1 RGD:13119… Rattus norve… #> 5 Homo sapiens HGNC:950 BAP1 in ortholo… UCH2 NCBIGene:… Arabidopsis … #> 6 Homo sapiens HGNC:950 BAP1 in 1 to 1 … Bap1 MGI:12065… Mus musculus #> 7 Homo sapiens HGNC:950 BAP1 in 1 to 1 … BAP1 NCBIGene:… Bos taurus #> 8 Homo sapiens HGNC:950 BAP1 in paralog… UCHL1 HGNC:12513 Homo sapiens #> 9 Homo sapiens HGNC:950 BAP1 in 1 to 1 … bap1 Xenbase:X… Xenopus (Sil… #> 10 Homo sapiens HGNC:950 BAP1 in 1 to 1 … BAP1 NCBIGene:… Pan troglody… #> 11 Homo sapiens HGNC:950 BAP1 in 1 to 1 … BAP1 NCBIGene:… Monodelphis … #> 12 Homo sapiens HGNC:950 BAP1 in 1 to 1 … BAP1 NCBIGene:… Sus scrofa #> 13 Homo sapiens HGNC:950 BAP1 in 1 to 1 … BAP1 NCBIGene:… Macaca mulat… #> 14 Homo sapiens HGNC:950 BAP1 in ortholo… UCH1 NCBIGene:… Arabidopsis … #> 15 Homo sapiens HGNC:950 BAP1 in 1 to 1 … bap1 NCBIGene:… Anolis carol… #> 16 Homo sapiens HGNC:950 BAP1 in ortholo… bap1 ZFIN:ZDB-… Danio rerio #> 17 Homo sapiens HGNC:950 BAP1 in 1 to 1 … calyp… FlyBase:F… Drosophila m… #> # ... with 3 more variables: evidence <fct>, publications <fct>, #> # provided_by <fct> #> #> $response #> <monarch https://api.monarchinitiative.org/api/bioentity/gene/NCBIGene%3A8314/homologs/?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': 17 obs. of 14 variables: #> ..$ provided_by :List of 17 #> ..$ relation :'data.frame': 17 obs. of 2 variables: #> ..$ object_extensions : logi [1:17] NA NA NA NA NA NA ... #> ..$ publications :List of 17 #> ..$ object :'data.frame': 17 obs. of 3 variables: #> ..$ negated : logi [1:17] FALSE FALSE FALSE FALSE FALSE FALSE ... #> ..$ slim : logi [1:17] NA NA NA NA NA NA ... #> ..$ subject_extensions: logi [1:17] NA NA NA NA NA NA ... #> ..$ type : logi [1:17] NA NA NA NA NA NA ... #> ..$ qualifiers : logi [1:17] NA NA NA NA NA NA ... #> ..$ evidence_graph :'data.frame': 17 obs. of 2 variables: #> ..$ evidence_types : logi [1:17] NA NA NA NA NA NA ... #> ..$ id : chr [1:17] "beb2860f-b6ab-472e-8c77-eb8ff2a5da99" "47931d07-86d6-40a2-82d8-d7919a0e8ad5" "5eea0259-b923-49f5-a344-86820defa027" "bfe3507a-f8bf-4a7d-949b-ab3e63dd8e95" ... #> ..$ subject :'data.frame': 17 obs. of 3 variables: #> $ objects : chr [1:17] "FlyBase:FBgn0262166" "HGNC:12513" "HGNC:12515" "HGNC:19678" ... #> $ highlighting : NULL #> $ numFound : NULL #> $ facet_counts :List of 2 #> ..$ subject_taxon_label:List of 1 #> ..$ object_closure :List of 25 #> $ docs : NULL #>