[Bioc-devel] A question on IRanges package

I'll look at the code. As far as tracking line numbers, no, because the
code is bundled into a package -- there are no files anymore. In principle,
that could be improved, but as far as I know, it hasn't been. If you're

trying to figure out dispatch behavior, things like
selectMethod(findOverlaps, c("GRanges, "GRanges")) and trace(findOverlaps,
browser, sig=c("GRanges", "GRanges")) are your friend.

Michael


On Thu, Apr 3, 2014 at 4:22 PM, Yuan Luo <yuan.hypnos.luo at gmail.com> wrote:

At the moment I am using the package to tweak some design on interval tree
algorithm, and much of my efforts are hack. So does the code suggest to you
what I am doing wrong to get the match.arg failing error?
Also, when you were developing the package, how do you tell the traceback
to show line numbers and file names. My googling seems to suggest it's hard
to do so in R, but I figured gurus may see better.

Best,
Yuan


On Thu, Apr 3, 2014 at 6:05 PM, Michael Lawrence <
lawrence.michael at gene.com> wrote:

It looks like the only hits this will filter out are cases where the
start of the query (X) is equal to the end of the subject (Y), but it seems
like the "o" operation is different -- it requires that X start before Y
starts and end before Y ends.

We could add these relations to IRanges, but maybe findOverlaps is not
the right place. Instead, we could have an %o% operator, plus operators for
the rest of the algebra. But maybe it would help to hear your use case.

Michael



On Thu, Apr 3, 2014 at 1:13 PM, Yuan Luo <yuan.hypnos.luo at gmail.com>wrote:

Hi Michael,
Thanks for your reply! I covered setGeneric as well, attached is the
modified code.
My change is pretty simple, I want to support the o relation in Allen's
Interval algebra (http://en.wikipedia.org/wiki/Allen's_interval_algebra)
So I added one more filter option
     } else if (type == "o") {
         m <- m[start(query)[m[,1L]] < end(subject)[m[,2L]], , drop=FALSE]
     }

 From the stack trace, I suspect the method
definition setMethod("findOverlaps", c("RangesList", "IntervalForest"),
is not called upon, and the error happens before that, but since the
stack trace doesn't tell me in which file and which line each frame is, I
am a bit clueless. Is there anyway to reveal that information?

Best,
Yuan


On Thu, Apr 3, 2014 at 3:57 PM, Michael Lawrence <
lawrence.michael at gene.com> wrote:

On Thu, Apr 3, 2014 at 11:33 AM, Yuan Luo <yuan.hypnos.luo at gmail.com>wrote:

Hi All,
Sorry for possible spam, but I am trying to customize IRanges package
locally. For what I am doing, I introduced another option to type
parameters to the findOverlaps method. In the file
findOverlaps-methods.R,
I modified every instance of
type = c("any", "start", "end", "within", "equal"),
into
type = c("any", "start", "end", "within", "equal", "o"),

I'm curious as to what "o" is supposed to do and wonder whether you
really need to be making this modification. Tough to help without seeing
any of your code. Probably, you just missed one, maybe the generic itself?

Michael

But when I call
h = findOverlaps(varanges, rna_tree, type="o")

I got the error

h = findOverlaps(varanges, rna_tree, type="o")

Error in match.arg(type) :
   'arg' should be one of "any", "start", "end", "within", "equal"
with the following traceback information

traceback()

5: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices),
        collapse = ", ")), domain = NA)
4: match.arg(type)
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(varanges, rna_tree, type = "o")
1: findOverlaps(varanges, rna_tree, type = "o")

Is there any place that I missed where there is a default type vector
specification?
Also, how do you guys get R to display filename and line numbers for
the
methods in the traceback stack?

Best,
Yuan

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