Thanks Steve. Yes, the docs had it backwards. It was already fixed in devel;
I just pushed it back to release. Sorry that this consumed your time.

Michael

On Tue, Dec 28, 2010 at 9:28 AM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> I think the holiday-over-eating is affecting my reading comprehension
> skills. I'm having problems groking the documentation/functionality of
> (for instance) precede, as it seems to return an integer vector that's
> "backwards to" the documentation.
>
> For instance, for `precede(x, subject)`, the docs say:
>
>  precede returns an integer vector of the index of range in subject
>  that ends before and closest to the start of each range in x. Note
>  that any overlapping ranges are excluded. NA is returned when there
>  are no qualifying ranges in subject.
>
> I am expecting an integer vector that is as long as x that indexes
> *into* the subject ranges. I'm getting that, but I also expect that
> the i'th value of the returned integer vector should be the index into
> `subject` that is closest to and precedes the i'th range in x.
>
> Using the second example from the docs, we don't get this at all ...
> in fact we get something of the opposite:
>
>  query <- IRanges(c(1, 3, 9), c(3, 7, 10))
>  subject <- IRanges(c(3, 2, 10), c(3, 13, 12))
>
>  p <- precede(query, subject) # c(3L, 3L, NA)
>
> The way I'm reading the docs, shouldn't p[1] indicate that
> subject[p[1]] "ends before and [is] closest to" query[1]? The returned
> vector is rather telling me that query[1] precedes subject[p[1]].
>
> So, shouldn't the docs read something more like "precede returns an
> integer vector of the index into the range of `subject` that
> immediately follows the corresponding range in x (the query) ...
> overlaps ignored, etc." Or something similar, no?
>
> R> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] IRanges_1.8.7
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.1
>
> Thanks,
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact<http://cbio.mskcc.org/%7Elianos/contact>
>
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