AnnotationHub has no (not all) data
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@mario-dejung-7959
Last seen 3.1 years ago
Germany

Hi all, 

I just started playing with AnnotationHub and running into some problems.

I downloaded the package and updated the recommended ones and started to follow the manual.

 

> library(AnnotationHub)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

.........

> ah <- AnnotationHub()
updating metadata from server...
> ah
class: AnnotationHub
length: 10780
filters: none
hubUrl: http://annotationhub.bioconductor.org/ah
snapshotVersion: 2.14/1.4.0; snapshotDate: 2014-05-15
hubCache: /Users/madejung/.AnnotationHub 


​So there seems to be no (not much) data inside the hub object. Also the ah$dataprovider does not exist.

> str(ah)
Formal class 'AnnotationHub' [package "AnnotationHub"] with 6 slots
  ..@ hubUrl         : chr "http://annotationhub.bioconductor.org/ah"
  ..@ hubCache       : chr "/Users/madejung/.AnnotationHub"
  ..@ snapshotVersion: chr "2.14/1.4.0"
  ..@ snapshotDate   : POSIXlt[1:1], format: "2014-05-15"
  ..@ snapshotPaths  : Named chr [1:10780] "ensembl/release-69/fasta/ailuropoda_melanoleuca/pep/Ailuropoda_melanoleuca.ailMel1.69.pep.all.fa.rz" "ensembl/release-69/fasta/anolis_carolinensis/cdna/Anolis_carolinensis.AnoCar2.0.69.cdna.all.fa.rz" "ensembl/release-69/fasta/anolis_carolinensis/pep/Anolis_carolinensis.AnoCar2.0.69.pep.all.fa.rz" "ensembl/release-69/fasta/bos_taurus/cdna/Bos_taurus.UMD3.1.69.cdna.all.fa.rz" ...
  .. ..- attr(*, "names")= chr [1:10780] "ensembl.release.69.fasta.ailuropoda_melanoleuca.pep.Ailuropoda_melanoleuca.ailMel1.69.pep.all.fa.rz" "ensembl.release.69.fasta.anolis_carolinensis.cdna.Anolis_carolinensis.AnoCar2.0.69.cdna.all.fa.rz" "ensembl.release.69.fasta.anolis_carolinensis.pep.Anolis_carolinensis.AnoCar2.0.69.pep.all.fa.rz" "ensembl.release.69.fasta.bos_taurus.cdna.Bos_taurus.UMD3.1.69.cdna.all.fa.rz" ...
  ..@ filters        : list()
> 

Any suggestion why this happens or what I can do?

annotation bioconductor • 1.5k views
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barashe ▴ 10
@barashe-8770
Last seen 5.9 years ago
European Union

Don't know if still relevant, but you need to install/update "interactiveDisplayBase".
Type biocLite("interactiveDisplayBase")

That solved it for me.
 

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 5 months ago
United States

I would recommend updating to R-3.2. The AnnotationHub package has been completely revamped and many more resources are available (newly added resources will not be available to you unless you update). The new version has 34059 resources compared to 10780 in your version. Consult the man pages and vignettes in the new version because the API has changed too (it's simpler). One of the things that's changed is there is no tab-completion on the AnnotationHub object; instead there is a query() function that lets you do a Google-type search that searches all relevant fields. BTW, ah is an S4 class, so tab completion on ah$ will not show you its slots (plus the version of AnnotationHub you're using has special tab-completion behavior associated with $ in any case). DataProvider is a column in the ah metadata. In your version of AnnotationHub you can look at the possible values for DataProvider this way:

keys(ah, keytype="DataProvider")

But I highly recommend you upgrade.

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@mario-dejung-7959
Last seen 3.1 years ago
Germany

Hi Dan,

Thanks for your fast response. I upgraded and now the ah object looks almost like in the tutorial. Just one thing is problematic now.

The tutorial has a line which says sah <- display(ah) which produces an error:

sah <- display(ah)
shiny::dataTableOutput is deprecated. Please use DT::dataTableOutput instead. To disable this message, run options(shiny.deprecation.messages=FALSE) (Last used in version 0.11.1)

Listening on http://127.0.0.1:5557
Error in loadNamespace(name) : there is no package called ‘rstudio’

I updated also to RStudio 0.99.441 in the whole update procedure... Not sure where this error is coming from. I searched for matching packages to install and installed rstudioapi which didn't solved the problem.

Any suggestion?

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Are you running the commands within the RStudio console? What happens if you try the same thing in a normal R console?

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Hi Keith, I was running within RStudio. Testes outside and it worked without problems. Thanks for the hint, but I have no idea how to fix this. :-)

 

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