[Bioc-devel] Suggestion: export function fetchChromLengthsFromEnsembl in GenomicFeatures

Hervé Pagès hpages at fredhutch.org
Sun Apr 12 08:11:26 CEST 2015

Hi jo,

getChromInfoFromBiomart() is a higher level function that is
exported, documented, and intended to be used by the user for
that, rather than internal helpers fetchChromLengthsFromEnsembl()
and fetchChromLengthsFromEnsemblPlants().

However, after some discussions here with Marc and Sonali, my
understanding is that the GRanges objects made from the Ensembl
GTF files are going to have their seqinfo updated soon so you
won't need that.


On 04/11/2015 12:37 PM, Rainer Johannes wrote:
> I wanted to ask whether it would be possible to export the functions "fetchChromLengthsFromEnsembl" and "fetchChromLengthsFromEnsemblPlants" in GenomicFeatures, as I find these methods quite useful to retrieve chromosome lengths.
> best, jo
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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