[Bioc-devel] mget and AnnDbBimap problem
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Tue Oct 4 21:30:59 CEST 2011
On Tue, Oct 4, 2011 at 3:21 PM, Paul Shannon
<pshannon at systemsbiology.org> wrote:
> There is a function in my RCytoscape package which fails on a call to mget when passed an AnnDbBimap ('org.Hs.egSYMBOL2EG'). The same mget call works fine in client code. I figure this is caused by package structure, NAMESPACE, or something related. But I cannot figure it out.
> client code: tbls.trompeter <- read.interactions ('trompeter.tsv', org.Hs.egSYMBOL2EG)
> error from package: Error in mget(toupper(node.names), name.map, ifnotfound = NA): second argument must be an environment
> executing this: name.lookup.tbl <- mget (toupper (node.names), name.map, ifnotfound=NA)
> from function defined: read.interactions <- function (filename, name.map)
Are you sure `name.map` is what you think it is in your method? Maybe
you can drop a call to `browser()` in your code to make sure name.map
is a bimap thing?
If `name.map` is what you expect it to be, maybe doing something like
`AnnotationDbi::mget(toupper(..), name.map, ...)` would work?
Graduate Student: Computational Systems Biology
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| Weill Medical College of Cornell University
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