[BioC] exon genomic coordinates

Martin Morgan mtmorgan at fhcrc.org
Fri Nov 22 00:05:57 CET 2013


On 11/21/2013 02:53 PM, array chip wrote:
> Thanks Martin. I am using R3.0.0 on a PC.

yes, sorry, same story -- update R (recommended) or install tools to build 
packages from source.

Martin

>
> John
>
> --------------------------------------------------------------------------------
> *From:* Martin Morgan <mtmorgan at fhcrc.org>
> *To:* array chip <arrayprofile at yahoo.com>; Michael Lawrence
> <lawrence.michael at gene.com>
> *Cc:* "bioconductor at r-project.org" <bioconductor at r-project.org>
> *Sent:* Thursday, November 21, 2013 2:40 PM
> *Subject:* Re: [BioC] exon genomic coordinates
>
> On 11/21/2013 02:21 PM, array chip wrote:
>  > Thank you Michael. I got an error message when running:
>  >
>  >> library(Homo.sapiens)
>  > Loading required package: GO.db
>  > Error : .onLoad failed in loadNamespace() for 'GO.db', details:
>  > Â  call: get(name, envir = asNamespace(pkg), inherits = FALSE)
>  > Â  error: object '.setDummyField' not found
>  > Error: package ‘GO.db’ could not be loaded
>
> I'm guess that you're using a mac and R-3.0.0
>
> You'll need to either update your R to the current release R-3.0.2 or install
> the software needed to build R packages from source and update all of your
> packages using type="source". It's easier to update your R, so I won't provide
> instructions for the latter.
>
> The problem is that a backward incompatibility was introduced in the methods
> package going from R-3.0.0 to R-3.0.1. The incompatibility means that the
> Macintosh binaries we (Bioconductor) build with the current R only work with
> versions of R after the incompatiblity was introduced. So you either need to use
> a current R, or build the packages yourself.
>
> Martin
>
>  >
>  >
>  > I already re-installing GO.db package, but still got the same error:
>  >
>  >> biocLite("GO.db")
>  > BioC_mirror: http://bioconductor.org <http://bioconductor.org/>
>  > Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.0.
>  > Installing package(s) 'GO.db'
>  > trying URL
> 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/GO.db_2.9.0.zip'
> <http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/GO.db_2.9.0.zip%27>
>  > Content type 'application/zip' length 25091062 bytes (23.9 Mb)
>  > opened URL
>  > downloaded 23.9 Mb
>  >
>  >
>  > John
>  >
>  >
>  > ________________________________
>  >  From: Michael Lawrence <lawrence.michael at gene.com
> <mailto:lawrence.michael at gene.com>>
>  >
>  > Cc: "bioconductor at r-project.org <mailto:bioconductor at r-project.org>"
> <bioconductor at r-project.org <mailto:bioconductor at r-project.org>>
>  > Sent: Thursday, November 21, 2013 7:43 AM
>  > Subject: Re: [BioC] exon genomic coordinates
>  >
>  >
>  >
>  > Assuming human, use the Homo.sapiens package:
>  >
>  >
>  > library(Homo.sapiens)
>  > id <- select(Homo.sapiens, "KIT", "ENTREZID", "SYMBOL")$ENTREZID
>  > exons(Homo.sapiens, list(gene_id = id))
>  >
>  > It would be a lot nicer if exons() could take the gene symbol directly, but
> I've long given up trying to request that.
>  >
>  > The nice thing about this approach is that you have a GRanges, and you're not
> off in data.frame land.
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  > Hi,
>  >>
>  >>
>  >> Can anyone suggest how to retrieve the genomic coordinates for all exons for
> a given gene by say gene symbol? For example, how to retrieve the coordinates
> for all 21 exons for gene KIT?
>  >>
>  >> Thanks
>  >>
>  >> John
>  >> Â  Â  Â  Â  [[alternative HTML version deleted]]
>  >>
>  >> _______________________________________________
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>  >>
>  >     [[alternative HTML version deleted]]
>  >
>  >
>  >
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>
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> 1100 Fairview Ave. N.
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>
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>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



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