R/monarchr.R
bioentity_exp_anatomy_assoc_w_gene.Rd
Given a gene, what expression anatomy is associated with it.
bioentity_exp_anatomy_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 anatomy information, monarch_api S3 class).
https://api.monarchinitiative.org/api/bioentity/gene/NCBIGene
gene <- "NCBIGene:8314" bioentity_exp_anatomy_assoc_w_gene(gene)#> $anatomy #> # 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 expresse… vastus la… UBERON:0… NA #> 2 Homo sapiens HGNC:950 BAP1 expresse… central n… UBERON:0… NA #> 3 Homo sapiens HGNC:950 BAP1 expresse… nucleus a… UBERON:0… NA #> 4 Homo sapiens HGNC:950 BAP1 expresse… layer of … UBERON:0… NA #> 5 Homo sapiens HGNC:950 BAP1 expresse… paraflocc… UBERON:0… NA #> 6 Homo sapiens HGNC:950 BAP1 expresse… Brodmann … UBERON:0… NA #> 7 Homo sapiens HGNC:950 BAP1 expresse… parietal … UBERON:0… NA #> 8 Homo sapiens HGNC:950 BAP1 expresse… putamen UBERON:0… NA #> 9 Homo sapiens HGNC:950 BAP1 expresse… Brodmann … UBERON:0… NA #> 10 Homo sapiens HGNC:950 BAP1 expresse… gingival … UBERON:0… NA #> 11 Homo sapiens HGNC:950 BAP1 expresse… amygdala UBERON:0… NA #> 12 Homo sapiens HGNC:950 BAP1 expresse… quadricep… UBERON:0… NA #> 13 Homo sapiens HGNC:950 BAP1 expresse… bone marr… UBERON:0… NA #> 14 Homo sapiens HGNC:950 BAP1 expresse… lung UBERON:0… NA #> 15 Homo sapiens HGNC:950 BAP1 expresse… primary v… UBERON:0… NA #> 16 Homo sapiens HGNC:950 BAP1 expresse… tonsil UBERON:0… NA #> 17 Homo sapiens HGNC:950 BAP1 expresse… occipital… UBERON:0… NA #> 18 Homo sapiens HGNC:950 BAP1 expresse… metanephr… UBERON:0… NA #> 19 Homo sapiens HGNC:950 BAP1 expresse… parotid g… UBERON:0… NA #> 20 Homo sapiens HGNC:950 BAP1 expresse… adipose t… UBERON:0… NA #> # ... with 3 more variables: evidence <fct>, publications <fct>, #> # provided_by <fct> #> #> $response #> <monarch https://api.monarchinitiative.org/api/bioentity/gene/NCBIGene%3A8314/expression/anatomy?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 : logi [1:20] NA NA NA NA NA NA ... #> ..$ 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] "41017a0d-7cb1-4f51-826e-ea68c527ed68" "6a454c61-028a-4cd9-8720-bb1468803ddb" "12847f51-9540-4158-9a2a-9cf4fdca8099" "e6a4b39a-f9e4-40bd-9e92-53e7b955679e" ... #> ..$ subject :'data.frame': 20 obs. of 3 variables: #> $ objects : chr [1:20] "UBERON:0001017" "UBERON:0001377" "UBERON:0001379" "UBERON:0001831" ... #> $ highlighting : NULL #> $ numFound : NULL #> $ facet_counts :List of 2 #> ..$ subject_taxon_label:List of 1 #> ..$ object_closure :List of 25 #> $ docs : NULL #>