[BioC] problems getting new intact networks from ppiData
Sara JC Gosline
sara.gosline at mail.mcgill.ca
Wed Dec 2 21:47:34 CET 2009
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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