Dear List
I have a very basic question on Rbiopaxparser.

Is it possible to extract from a biopax pathway imported with Rbiopaxparser
a subnetwork of all the interactions of a protein?
I'm able to select all the instances with the name of a protein of
interest. Then I try with getNeighborood function without any success...
Any advice it could be very helpful (including advices on other R tools
that can be more useful for my purpose)
thank you
Guido
Here is my code


library(rBiopaxParser)

#read a biopax file downloaded from NCI (url:
http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=betacatenin_deg_pathway&pathway_name=Degradation%20of%20beta%20catenin&source=NCI-Nature%20curated&what=graphic&jpg=on&ppage=1
biopax<-readBiopax("betacatenin_deg_pathway.owl")


pw_1 = selectInstances(biopax, class="protein", name="WNT3A")

b<-getNeighborhood(biopax,pw_1$id[1])

Have a look at the source of getNeighborhood ... better contact the developer

> getNeighborhood

function (biopax, id, depth = 1, onlyInPathways = c(), biopaxlevel = 3) 

{

    return(NULL)

}

<environment: namespace:rBiopaxParser>

> sessionInfo()

R version 3.1.1 (2014-07-10)

Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats     graphics  grDevices datasets  utils     tools     methods  

[8] base     

other attached packages:

[1] rBiopaxParser_2.5.0  data.table_1.9.4     rmarkdown_0.3.8     

[4] knitr_1.6            weaver_1.31.0        codetools_0.2-9     

[7] digest_0.6.4         BiocInstaller_1.15.5

loaded via a namespace (and not attached):

[1] chron_2.3-45    evaluate_0.5.5  formatR_1.0     htmltools_0.2.6

[5] plyr_1.8.1      Rcpp_0.11.3     reshape2_1.4    stringr_0.6.2  

[9] XML_3.98-1.1