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BioPAX / paxtoolsr

The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database
https://bioconductor.org/packages/release/bioc/html/paxtoolsr.html
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Error while running topPathways() #8

Open Kamalika17 opened 1 year ago

Kamalika17 commented 1 year ago

Hi,

I am trying to get all the pathways associated with a the gene: ADCYAP1R1.

topPathways(q="ADCYAP1R1", organism='9606')

However, I am getting the following error:

"Error in [.data.frame(resultsDf, , c("uri", "biopaxClass", "name", "dataSource")) : undefined columns selected"

I see that this particular gene has 3 pathways mentioned in http://www.pathwaycommons.org/.

I am using R 3.6.0 and I have installed the paxtoolsr package using Biocmanager.

Please help me with this.

Thanks in advance.

cannin commented 1 year ago

@Kamalika17 the error results because there are no hits. I should write a better error message. For you, right now, if you run this command with "verbose=TRUE": 

topPathways(q="ADCYAP1R1", organism='9606', verbose=TRUE)

it will show you the API call generated: http://www.pathwaycommons.org/pc2/top_pathways?q=ADCYAP1R1&organism=9606

Going to that link, you can see that no hits were returned: 

<searchResponse numHits="0" maxHitsPerPage="0" pageNo="0" comment="Top Pathways (technically, each has empty index field 'pathway'; that also means, they are neither components of other pathways nor controlled of any process)" version="12"/>
Kamalika17 commented 1 year ago

Hi @cannin,

Thank you very much.

In that case, I think it is generating wrong result because when I search the "PathwayCommons12.All.hgnc.gmt", I see "ADCYAP1R1" has the following pathways associated with it:

"http://identifiers.org/reactome/R-HSA-187024", "http://identifiers.org/reactome/R-HSA-418555", "http://identifiers.org/reactome/R-HSA-420092"

Is this correct or am I missing something?

Thanks

cannin commented 1 year ago

I'll have to forward this question to other members of the team since R is just returning results from the Pathway Commons API. In the meantime, using the GMT file to get relevant pathways is probably best.