[BioC] Problems with section 3.4 in vignette GenomicRangesUseCases.pdf

[Valerie Obenchain]

Hi Yue,

Yes, the vignette was incorrect. It has been fixed in version 1.8.4 in 
release and 1.9.9 in the devel branch. These versions should be 
available in ~24 hours through biocLite() or now from the svn 
repositories. Thanks for pointing out this bug and sorry we missed the 
previous discussion of the topic.

We would suggest using

     not.exons <- aligns[!aligns %in% exonRanges]

as posted in the last thread.

Valerie





The vignette has been updated in release devel 1.9.9


On 04/24/2012 06:52 PM, Yue Li wrote:
> Dear List,
>
> This is a question that has been asked before in the message titled "GenomicRanges Use Cases - subsetByOverlaps". But I just want to confirm that there is a mistake in section 3.4 of the vignette GenomicRangesUseCases.pdf.
>
> Basically, it was claimed in the section to look for "ranges that did not overlap with any of the known exons from Saccharomycess cerevisiae." using:
>
> filtData<- subsetByOverlaps(aligns, exonRanges)
>
> However, filtData in fact contains exactly the read regions that DO overlap with the known exons.
>
> To get ""ranges that did not overlap with any of the known exons", it's been suggested in that thread to instead use:
>
> not.exons<- aligns[!aligns %in% exonRanges]
>
> Is the latter in fact the CORRECT way to do it or the way in the vignette?
>
> Thanks in advance!
> Yue
>
>
> 	[[alternative HTML version deleted]]
>
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