Asking for a friend :) The vignette [1] seems not completely explicit about this, and the example [2] contains mandatory-looking(?) columns RDataClass, DispatchClass, RDataPath. [1] https://www.bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html [2] https://github.com/Bioconductor/GSE62944/blob/master/inst/extdata/metadata.csv With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de My book with Susan Holmes: http://www.huber.embl.de/msmb
[Bioc-devel] Can ExperimentHub packages contain non-R data formats?
2 messages · Wolfgang Huber, Shepherd, Lori
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. RDataClass, DispatchClass RDataPath 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 at r-project.org> on behalf of Wolfgang Huber <wolfgang.huber at embl.de>
Sent: Tuesday, September 11, 2018 5:29:55 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Can ExperimentHub packages contain non-R data formats?
Sent: Tuesday, September 11, 2018 5:29:55 PM
To: bioc-devel at 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. [1] https://www.bioconductor.org/packages/devel/bioc/vignettes/ExperimentHub/inst/doc/CreateAnExperimentHubPackage.html [2] https://github.com/Bioconductor/GSE62944/blob/master/inst/extdata/metadata.csv With thanks in advance- Wolfgang ------- Wolfgang Huber Principal Investigator, EMBL Senior Scientist European Molecular Biology Laboratory (EMBL) Heidelberg, Germany wolfgang.huber at embl.de http://www.huber.embl.de My book with Susan Holmes: http://www.huber.embl.de/msmb _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.