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


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