[Bioc-devel] A question on IRanges package
On 04/03/2014 06:17 PM, Yuan Luo wrote:
A side question, in the frame 3, what does .local mean? local environment? like if I go into frame 3, I'd be able to print out their values?
(I'm only the messenger) .local is a nested function created when a method adds
arguments to the generic. After
setGeneric("foo", function(x, ...) standardGeneric("foo"))
setMethod("foo", "A", function(x, ...) x)
setMethod("foo", "B", function(x, y, ...) { x })
compare
> selectMethod("foo", "A")
Method Definition:
function (x, ...)
x
Signatures:
x
target "A"
defined "A"
> selectMethod("foo", "B")
Method Definition:
function (x, ...)
{
.local <- function (x, y, ...)
{
x
}
.local(x, ...)
}
Signatures:
x
target "B"
defined "B"
so .local appears on the call stack (after the generic and method, so for
findOverlaps(IRanges(), IRanges(), type="o") we have in part
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(IRanges(), IRanges(), type = "o")
1: findOverlaps(IRanges(), IRanges(), type = "o")
corresponding, in reverse order, to the generic, the method, and the nested
function).
On Thu, Apr 3, 2014 at 9:10 PM, Yuan Luo <yuan.hypnos.luo at gmail.com
<mailto:yuan.hypnos.luo at gmail.com>> wrote:
I think that line at 4 points to the generic definition, at least on my
machine (and keep source works, thanks!).
Just found what was the culprit, there is a wrapper in
findOverlaps-GIntervalTree-methods.R#12. After updating that, it works.
> traceback()
5: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices),
collapse = ", ")), domain = NA)
4: match.arg(type) at findOverlaps-GIntervalTree-methods.R#12
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(varanges, rna_tree, type = "o") at findOverlaps-methods.R#14
1: findOverlaps(varanges, rna_tree, type = "o")
Again, thank you both!
Best,
Yuan
On Thu, Apr 3, 2014 at 7:49 PM, Martin Morgan <mtmorgan at fhcrc.org
<mailto:mtmorgan at fhcrc.org>> wrote:
On 04/03/2014 04:42 PM, Michael Lawrence wrote:
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
I think there's an option, set in .Rprofile or as an environment
variable described in ?options,
options(keep.source.pkgs=TRUE)
that annotates the source of installed packages with line numbers, e.g.,
after doing this and then installing GenomicRanges (on my own version)
> library(GenomicRanges)
> findOverlaps(GRanges(), GRanges(), type="o")
Error in match.arg(type) :
'arg' should be one of "any", "start", "end", "within", "equal"
> traceback()
5: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices),
collapse = ", ")), domain = NA)
4: match.arg(type) at findOverlaps-methods.R#63
3: .local(query, subject, maxgap, minoverlap, type, select, ...)
2: findOverlaps(GRanges(), GRanges(), type = "o")
1: findOverlaps(GRanges(), GRanges(), type = "o")
I'm not really sure which lines are annotated with source information.
Martin
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
<mailto: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 <mailto: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
<mailto: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
<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
<mailto:lawrence.michael at gene.com>> wrote:
On Thu, Apr 3, 2014 at 11:33 AM, Yuan Luo
<yuan.hypnos.luo at gmail.com
<mailto: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
[[alternative HTML version deleted]]
_________________________________________________
Bioc-devel at r-project.org
<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/__listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
[[alternative HTML version deleted]]
_________________________________________________
Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/__listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793