[BioC] problems getting new intact networks from ppiData

Sara JC Gosline sara.gosline at mail.mcgill.ca
Thu Dec 3 22:43:51 CET 2009


Hi Tony,

Thanks for your prompt response.  This package was exactly what I 
needed, though after trying out the package for a day I have another 
question.

The function translateID refers to another function translateID-methods 
to describe the precise capabilities, but when I type 
?translateID-methods I get the man page for the arithemetic operators.  
 From trying various types of identifiers it appears that there are only 
three supported identifiers: Sourceid (a number?), Intact and 
UniprotKB.  Is this true?

thanks again for your help!
sara

Tony Chiang wrote:
> Hi Sara,
>
> A big mea culpa on my part here. I meant to deprecate the ppiData 
> package as it is no longer necessary. When I first started this work, 
> I had some ad hoc functions to parse the IntAct repository. There is 
> now the RpsiXML package where the user can parse the XML data files to 
> get the latest interaction data sets. This way there is no longer a 
> need for me to parse the XML files and put the data into the R data 
> repository.
>
> The first thing you will need to do is update your R to the current 
> release. Then make the following calls:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("RpsiXML")
>
> The package vignette should be a good resource to help you start 
> parsing the XML data files you would like. Some shameless 
> self-promotion here as well to help with obtaining the data you need 
> and some statistical applications for the data:
>
> http://www.nature.com/nprot/journal/v4/n4/full/nprot.2009.26.html
>
> Cheers,
> --Tony
>
> On Wed, Dec 2, 2009 at 12:47 PM, Sara JC Gosline 
> <sara.gosline at mail.mcgill.ca <mailto:sara.gosline at mail.mcgill.ca>> wrote:
>
>     Hello,
>
>     I'm trying to use the ppiData package and am having trouble
>     getting newer datasets from intact.
>     >library(ppiData)
>     >collectIntactPPIData("EBI-2007879")
>     Error in b2pList[[i]][[j]] : subscript out of bounds
>
>     My sessionInfo() is at the end of this email.
>
>     It appears that this later dataset is not in the downloaded
>     repository. The man pages refer to this tableList.rda which is
>     generated by parseIntAct.R.  I found parsingIntAct.R but the
>     output doesn't appear to match tableList.rda.
>     Is there a simple way to use this package to access datasets that
>     are not in tableList.rda?
>
>     thanks,
>     sara
>
>
>     > sessionInfo()
>     R version 2.7.0 (2008-04-22)
>     x86_64-unknown-linux-gnu
>
>     locale:
>     LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
>     attached base packages:
>     [1] grid      stats     graphics  grDevices utils     datasets
>      methods
>     [8] base
>
>     other attached packages:
>     [1] ppiData_0.1.13   Rgraphviz_1.18.0 graph_1.18.1
>
>     loaded via a namespace (and not attached):
>     [1] cluster_1.11.10 tools_2.7.0
>
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