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@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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