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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >