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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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Finding a pathway for a given gene #2

Closed premadh closed 8 years ago

premadh commented 8 years ago

As discussed here: https://www.biostars.org/p/188779/#191357 I was trying get the pathways to which a gene is involved. But when I execute

geneSets <- downloadPc2("Pathway Commons.7.All.GSEA.hgnc.gmt.gz")

I get the error Error in strsplit(tmp3, ";") : non-character argument

I looked into the function itself: Line 29

idx <- grepl(".gz", links)

Here idx becomes FALSE for all cases

print(links) gives :

href "http://www.pathwaycommons.org" href "#" href "/pc2/home;jsessionid=408C224190DDD16A0058C5FB82E780FE" href "/pc2/home;jsessionid=408C224190DDD16A0058C5FB82E780FE#search" href "/pc2/home;jsessionid=408C224190DDD16A0058C5FB82E780FE#get" href "/pc2/home;jsessionid=408C224190DDD16A0058C5FB82E780FE#traverse" href "/pc2/home;jsessionid=408C224190DDD16A0058C5FB82E780FE#graph" href "/pc2/home;jsessionid=408C224190DDD16A0058C5FB82E780FE#top_pathways" href "/pc2/home;jsessionid=408C224190DDD16A0058C5FB82E780FE#parameter_values" href "/pc2/datasources;jsessionid=408C224190DDD16A0058C5FB82E780FE" href "/pc2/downloads;jsessionid=408C224190DDD16A0058C5FB82E780FE" href "formats" href "http://www.pathwaycommons.org/archives/" href "http://www.biopax.org/paxtools" href "https://github.com/BioPAX/Paxtools/wiki/PatternBinaryInteractionFramework" href "https://pathwaycommons.github.io/cpath2/" href "http://baderlab.org/" href "http://www.sanderlab.org"

Consequently, tmp and tmp2 are both empty. Can this be fixed?

cannin commented 8 years ago

There are two issues here:

1: I fixed the strsplit() issue recently. Pathway Commons moved where files are hosted causing this issue. You need the latest development version from GitHub using devtools (check the README for instructions). The fixed will be on Bioconductor 3.3 soon.

2: Pathway Commons recently released a new version. If you run:

downloadPc2() You'll see the updated file names, making the command now: 

downloadPc2("PathwayCommons.8.All.GSEA.hgnc.gmt.gz")

Check the documentation if you want the older version.