[Bioc-devel] New ExperimentHub resource and some related questions

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Thu Dec 20 13:05:57 CET 2018

There is a DispatchClass  -  FilePath -  That will download the file and give you the path to the file in the cache location rather than loading it to the R session -  You then can use the file path in whatever read/load/etc method you deem fit.

RDataClass  - I would either say character or matrix - knowing that there will be instructions on how to load the data somewhere in your package -

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 Lu, Dongyi (Lambda) <dlu2 using caltech.edu>
Sent: Wednesday, December 19, 2018 8:42:39 PM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] New ExperimentHub resource and some related questions

Hi everyone,

I�m writing a package (biocViews SinigleCell) that converts files of the BUS format (standing for Barcode, UMI, Set, see https://www.biorxiv.org/content/early/2018/11/21/472571) into a sparse matrix in R that can be used in Seurat and SingleCellExperiment. In order to write the examples and the vignette, I�m also putting the data itself into a package for ExperimentHub. The data used here are some mixed human and mouse cells from 10x. Here are my questions:

  1.  In the documentation for `ExperimentHubData::makeExperimentHubMetadata`, the fields `RDataClass` and `DispatchClass` are required. However, this accompanying dataset package is meant to download text files (generated by command line tools outside R) to disk rather than into the R session, and it�s the job of the SingleCell package to converts the text files into a sparse matrix. There is a website documenting how the command line tools were used to generate the text files. So is this dataset still appropriate for ExperimentHub?
  2.  If it is appropriate, then what shall I put in `RDataClass` and `DispatchClass`?


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