[Bioc-devel] Can ExperimentHub packages contain non-R data formats?

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Wed Sep 12 13:07:06 CEST 2018

It depends on what you mean.  We include those as our load methods generally are loading files into R for immediate use by a package.


If using the Bioconductor ExperimentHub -

We can always create a new DispathClass if one existing isn't appropriate.

The RDataPath is really what we call the folder and file name on the server. We require it to be the packagename/<optional sub dir>/fileName.ext .  The files don't have to be hosted on our S3 as long as they are on a publically accessible site (This is controlled by location_prefix)

The RDataClass gives and idea of what the user will get back.  We recently added a DispathClass of FilePath so that raw files could be stored.  The output for using this DispathClass is character as you would only get a character representing the path to the raw file in the ExperimentHub cache.

Hope this helps.  Let me know if you need further assistance or any further questions.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Wolfgang Huber <wolfgang.huber using embl.de>
Sent: Tuesday, September 11, 2018 5:29:55 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] Can ExperimentHub packages contain non-R data formats?

Asking for a friend :)

The vignette [1] seems not completely explicit about this, and the
example [2] contains mandatory-looking(?) columns RDataClass,
DispatchClass, RDataPath.


With thanks in advance-


Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany

wolfgang.huber using embl.de

My book with Susan Holmes: http://www.huber.embl.de/msmb

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