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wikipathways / rWikiPathways

R package for WikiPathways API
https://r.wikipathways.org/
MIT License
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loading of BridgeDbR does not happen authomatically when using getXrefList() #13

Closed egonw closed 4 years ago

egonw commented 4 years ago

In this vignette, Section 4, when not explicitly loading BridgeDbR first, we get an error with getXrefList():

> library(rWikiPathways)
> getXrefList('WP554', getSystemCode('Ensembl'))
Error in getSystemCode("Ensembl") : 
  could not find function "getSystemCode"
> library(BridgeDbR)
Loading required package: rJava

Attaching package: ‘BridgeDbR’

The following object is masked from ‘package:methods’:

    getProperties

> getXrefList('WP554', getSystemCode('Ensembl'))
 [1] "ENSG00000092009" "ENSG00000100448" "ENSG00000100739" "ENSG00000105329"
 [5] "ENSG00000113889" "ENSG00000130234" "ENSG00000130368" "ENSG00000135744"
 [9] "ENSG00000143839" "ENSG00000144891" "ENSG00000151623" "ENSG00000159640"
[13] "ENSG00000164867" "ENSG00000168398" "ENSG00000179142" "ENSG00000180772"
[17] "ENSG00000182220"
egonw commented 4 years ago

@AlexanderPico, I will send a PR to update the vignette to make clear that getSystemCode() comes from BridgeDbR, okay? (Like in Section 3)