[Bioc-devel] Question about package development

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


library(AnnotationHub)

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.

https://bioconductor.org/packages/release/BiocViews.html#




Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

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.
Regards,
Ghiwa


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As Lori has noted Bioconductor users have access to many chain files
through AnnotationHub -- please
let us know if these are not sufficient for your needs.

 library(AnnotationHub)
ah = AnnotationHub()

query(ah, "chain")

AnnotationHub with 1513 records

# snapshotDate(): 2018-08-01

# $dataprovider: UCSC

# $species: Homo sapiens, Mus musculus, Bos taurus, Pan troglodytes, Danio
r...

# $rdataclass: ChainFile, GRanges

# additional mcols(): taxonomyid, genome, description,

#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,

#   rdatapath, sourceurl, sourcetype

# retrieve records with, e.g., 'object[["AH5097"]]'


            title

  AH5097  | Primate Chain/Net

  AH5098  | Placental Chain/Net

  AH5099  | Vertebrate Chain/Net

  AH5126  | Self Chain

  AH5229  | Chimp Chain/Net

  ...       ...

  AH15215 | sacCer3ToSacCer2.over.chain.gz

  AH15216 | sacCer2ToSacCer1.over.chain.gz

  AH15217 | sacCer2ToSacCer3.over.chain.gz

  AH15218 | sacCer1ToSacCer2.over.chain.gz

  AH15219 | sacCer1ToSacCer3.over.chain.gz

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.
Regards,
Ghiwa


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_______________________________________________
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https://stat.ethz.ch/mailman/listinfo/bioc-devel