# ReactomeContentService4R: an R interface for the Reactome Content Service
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[](https://travis-ci.com/reactome/ReactomeContentService4R)
<!-- badges: end -->
The `ReactomeContentService4R` package provides a wrapper for the Reactome Content Service.
## Installation
```
# 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](https://rstudio.com/products/rstudio/download/) on macOS, make sure the version is __>= 1.3.1056__.
## Documentation
- [__Vignette__](https://bioconductor.org/packages/release/bioc/vignettes/ReactomeContentService4R/inst/doc/ReactomeContentService4R.html)
- [__Reactome Content Service__](https://reactome.org/dev/content-service)
## Usage
Fetch the information for a Reactome object:
```r
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:
```r
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:
```r
exportImage(species = "9606", output = "fireworks", format = "jpg", quality = 8)
```
Find more examples in the [vignette](https://bioconductor.org/packages/release/bioc/vignettes/ReactomeContentService4R/inst/doc/ReactomeContentService4R.html)!
## Feedback
Any feedback is welcome! Feel free to open an [issue](https://github.com/reactome/ReactomeContentService4R/issues) on GitHub.
