As I as I know, the type should be one of "any", "start",
"end", "within",
"equal".
You are using a undefined type.
Best,
KK
On Thu, Apr 3, 2014 at 2:48 PM, Yuan Luo <yuan.hypnos.luo@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"),
>
> 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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>
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>
--
Qiang Kou
qkou@umail.iu.edu
School of Informatics and Computing, Indiana University
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