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
On Fri, Aug 3, 2018 at 4:23 AM, Ghiwa Khalil <ghiwa.kha...@lau.edu> wrote:
> 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
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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