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

[Yue Li]

Thanks Valerie.

Yue

On 2012-04-26, at 2:58 PM, Valerie Obenchain wrote:

> 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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>