On Fri, Apr 20, 2012 at 8:58 AM, Jeremiah Degenhardt <
degenhardt.jeremiah@gene.com> wrote:

> >
> >
> > There is an "ignore.strand" argument to findOverlaps, so we have a
> switch. I
> > have always thought that strand should be ignored by default in
> operations
> > like overlap detection, and only considered as a "direction" rather than
> as
> > separate in space. It's very useful for resize() and flank() to consider
> > strand, but not so useful for findOverlaps. The ignore.strand=FALSE in
> those
> > cases default would qualify for the eight circle if there were a Bioc
> > Inferno book. It's only the default that I argue with though, having the
> > capability to consider strand is useful.
>
> I had forgotten about the ignore.strand option, thanks for the
> reminder Michael. So, given that it's there I agree with you fully. It
> seems he default should be changed to TRUE for the Overlap functions
> and the precedes and follows as well.
>
>
Unfortunately damnation is permanent and it's unlikely we'll be able to
modify that default now.


> Note however, that this would not fully correct the issue in the
> predictCoding function as the function still needs to correctly
> reverse complement the varAllele to get the annotation correct.
>
> As a further note on how big of an issue this is, if you go to the
> BioC home page and look at the tutorial on "Using Bioconductor to
> annotate genetic variants" you will find that the example makes this
> exact mistake. The variants in the VCF are unstranded and two of the
> genes in the example are negative strand and one is positive.
> Following the code you will get incorrect annotations for all variants
> on the negative strand genes.
>
> Jeremiah
>
>
>
> --
> Jeremiah Degenhardt, Ph.D.
> Computational Biologist
> Bioinformatics and Computational Biology
> Genentech, Inc.
> degenhardt.jeremiah@gene.com
>

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