[Bioc-devel] Propose to pass `...` to as.data.frame, GenomicRanges

[Hervé Pagès]

On 04/26/2012 05:50 PM, Michael Lawrence wrote:
> Seems reasonable to me...
>

Yep. Steve, do you want to go ahead and commit that? (Note that
man/GRanges-class.Rd would also need to be adjusted.)

Thanks,
H.

> On Thu, Apr 26, 2012 at 5:17 PM, Steve Lianoglou<
> mailinglist.honeypot at gmail.com>  wrote:
>
>> Howdy,
>>
>> I was chasing some weird bug for a while which was due to a library I
>> use working differently w/ factors and the fact that a call to
>> as.data.frame(GRanges)  doesn't let you specify how you want to handle
>> stringsAsFactors for the character columns of the
>> GRanges at elementMetadata.
>>
>> What do you say to a change that passes `...` down to the
>> `as.data.frame(elementMetadata(x))` call in the following method def
>> (GenomicRanges-class.R#Line245) here so it becomes
>> `as.data.frame(elementMetadata(x), ...)` allowing us to control this
>> behavior:
>>
>> setMethod("as.data.frame", "GenomicRanges",
>>     function(x, row.names=NULL, optional=FALSE, ...)
>>     {
>>         ranges<- ranges(x)
>>         if (missing(row.names))
>>             row.names<- names(x)
>>         if (!is.null(names(x)))
>>             names(x)<- NULL
>>         data.frame(seqnames=as.factor(seqnames(x)),
>>                    start=start(x),
>>                    end=end(x),
>>                    width=width(x),
>>                    strand=as.factor(strand(x)),
>>                    as.data.frame(elementMetadata(x)), ##<-- here
>>                    row.names=row.names,
>>                    stringsAsFactors=FALSE)
>>     }
>> )
>>
>> -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
>>
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-- 
Hervé Pagès

Program in Computational Biology
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