The ReactomeContentService4R package provides a wrapper for the Reactome Content Service.
# Pick one
## from Bioconductor (>= 3.13)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ReactomeContentService4R")
## from github
devtools::install_github("reactome/ReactomeContentService4R")
remotes::install_github("reactome/ReactomeContentService4R")
⚠️ If you are using RStudio on macOS, make sure the version is >= 1.3.1056.
Fetch the information for a Reactome object:
library(ReactomeContentService4R) #> Connecting...welcome to Reactome v74! dbp <- query(id = 'R-HSA-879796') str(dbp, max.level = 1) #> List of 18 #> $ dbId : int 879796 #> $ displayName : chr "DBP [nucleoplasm]" #> $ stId : chr "R-HSA-879796" #> $ stIdVersion : chr "R-HSA-879796.1" #> $ created :List of 5 #> $ modified :List of 5 #> $ name : chr [1:3] "DBP" "D site-binding protein" "DBP_HUMAN" #> $ speciesName : chr "Homo sapiens" #> $ compartment :'data.frame': 1 obs. of 9 variables: #> $ producedByEvent:'data.frame': 1 obs. of 17 variables: #> $ species : int 48887 #> $ endCoordinate : int 325 #> $ referenceType : chr "ReferenceGeneProduct" #> $ startCoordinate: int 1 #> $ referenceEntity:List of 22 #> $ className : chr "Protein" #> $ inDisease : logi FALSE #> $ schemaClass : chr "EntityWithAccessionedSequence"
Retrieve physical entities that participate in a specific Reaction:
getParticipants("R-HSA-400342", retrieval = "PhysicalEntities")
#> dbId displayName stId
#> 1 5640173 ARNTL gene [nucleoplasm] R-HSA-5640173
#> 2 400353 ARNTL [cytosol] R-HSA-400353
#> 3 5663268 RORA:Coactivator:ARNTL gene [nucleoplasm] R-HSA-5663268
#> 4 5663269 NR1D1:heme:Corepressors:ARNTL gene [nucleoplasm] R-HSA-5663269
#> 5 427531 SIRT1 [nucleoplasm] R-HSA-427531
#> stIdVersion
#> 1 R-HSA-5640173.1
#> 2 R-HSA-400353.1
#> 3 R-HSA-5663268.1
#> 4 R-HSA-5663269.1
#> 5 R-HSA-427531.1
#> name
#> 1 ARNTL gene
#> 2 ARNTL, BMAL1, Aryl hydrocarbon receptor nuclear translocator-like protein 1, BMAL1_HUMAN
#> 3 RORA:Coactivator:ARNTL gene
#> 4 NR1D1:heme:Corepressors:ARNTL gene
#> 5 SIRT1, NAD-dependent deacetylase sirtuin-1, SIRT1_HUMAN
#> speciesName endCoordinate referenceType startCoordinate className
#> 1 Homo sapiens -1 ReferenceDNASequence 1 DNA Sequence
#> 2 Homo sapiens 626 ReferenceGeneProduct 1 Protein
#> 3 Homo sapiens NA <NA> NA Complex
#> 4 Homo sapiens NA <NA> NA Complex
#> 5 Homo sapiens 747 ReferenceGeneProduct 2 Protein
#> inDisease schemaClass isChimeric
#> 1 FALSE EntityWithAccessionedSequence NA
#> 2 FALSE EntityWithAccessionedSequence NA
#> 3 FALSE Complex FALSE
#> 4 FALSE Complex FALSE
#> 5 FALSE EntityWithAccessionedSequence NA
Export the human fireworks image:
exportImage(species = "9606", output = "fireworks", format = "jpg", quality = 8)
Find more examples in the vignette!
Any feedback is welcome! Feel free to open an issue on GitHub.
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