problems getting new intact networks from ppiData
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@sara-jc-gosline-3831
Last seen 9.6 years ago
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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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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Tony Chiang ▴ 570
@tony-chiang-1769
Last seen 9.6 years ago
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_IDEN TIFICATION=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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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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 > >
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@sara-jc-gosline-3831
Last seen 9.6 years ago
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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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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@sara-jc-gosline-3831
Last seen 9.6 years ago
Please ignore this email, this issue was already resolved. sorry, sara Sara JC Gosline 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_IDEN TIFICATION=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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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