[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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