[Bioc-devel] Question about package development

Shepherd, Lori Lori@Shepherd @ending from Ro@wellP@rk@org
Fri Aug 3 13:42:44 CEST 2018

You could see if there are any appropriate chain files provided in AnnotationHub (https://bioconductor.org/packages/release/bioc/html/AnnotationHub.html)


ah = AnnotationHub( )

query(ah, "chain file")

or investigate other packages that do similar functions or address a similar types of data - they might have data you could use for the example as well.


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 Ghiwa Khalil <ghiwa.khalil using lau.edu>
Sent: Friday, August 3, 2018 4:23:35 AM
To: bioc-devel using r-project.org
Subject: EXTERNAL: [Bioc-devel] Question about package development

To whom it may concern,

I am Ghiwa a research assistant at Dr.Pierre Khoeuiry bioinformatic's lab at the American University of Beirut.

We are currently building our package and we have a question, we hope you can help us with.

While writing the documentation for the function(.Rd file) the examples section is mandatory, but our function uses

chrom.sizes and chain files which should be user provided.

How can we address this while writing the example? Should we include a chrom.sizes file and a chain file in the inst folder
to allow the example to run? And the disadvantage of that would be that the package would be large since the chain file is a large file.

Any recommendations?

Thank you.

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