[BioC] Problems with section 3.4 in vignette GenomicRangesUseCases.pdf
Yue Li
gorillayue at gmail.com
Thu Apr 26 21:00:53 CEST 2012
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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