So the documentation is off. I have copied the package maintainer to this e-mail thread so that he might be able to fix the man pages. Quick answer to the supported IDs. The translateID method basically tries to work with the repositories. If a particular repository has annotated UniprotKB, Gene Names, Protein Names, SourceID, then the translateID method can map between the supported IDs. So the answer to your question is it depends. The supported IDs varies between datasets as well as between repositories. This makes things a bit hard if you want to make some cross repository data analysis. The default is the UniprotKB IDs. I would say keep these whilst you are doing the analysis (if the IDs are not relevant), and at the end, use the biomaRt package to map IDs from the UniprotKB to whatever else is supported in Biomart and Ensembl. On Thu, Dec 3, 2009 at 1:43 PM, Sara JC Gosline <sara.gosline@mail.mcgill.ca> wrote: > 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@mail.mcgill.ca <mailto: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=e n_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_ID ENTIFICATION=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@stat.math.ethz.ch <mailto:bioconductor@stat.math.ethz.ch> >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > [[alternative HTML version deleted]]