[BioC] GenomicRanges countOverlaps error

[Suraj Menon]

Hi Steve

Thanks very much for your response.

Yes I was indeed getting an error previously. 
However, I then updated the GenomicRanges devel version just before writing to the mailing list, and hadn't noticed that I was now getting just a warning instead of an error.

Cheers
-Suraj


-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
Sent: 07 September 2010 21:32
To: Suraj Menon
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GenomicRanges countOverlaps error

Hi Suraj,

On Tue, Sep 7, 2010 at 7:01 AM, Suraj Menon <Suraj.Menon at cancer.org.uk> wrote:
> Hi all
>
> I've been trying to use the GenomicRanges countOverlaps function. When I was using the release version of GenomicRanges, countOverlaps worked fine for coordinates from chromosomes 1-9, but gave me an error for the others.
>
> I switched to using the development version of GenomicRanges. The function now works for all chromosomes other than X and Y.
> Does anyone know a way around this?

I'm sorry, but I don't see what you're trying to get around?

Is it where you are querying with GRange from chrX and chrY here?

<snip>

>> ## chrX
>> gr <- GRanges(seqnames = Rle("chrX", length(yst)),
> +      ranges = IRanges(yst, width = ywd))
>> counts <- countOverlaps(gr, aligns)
> Warning message:
> In .local(query, subject, maxgap, minoverlap, type, select, ...) :
>  'query' and 'subject' do not use a similiar naming convention for seqnames
</snip>

The call to countOverlaps is simply (now) drawing your attention to
the fact that the seqnames of your query and subject GRanges aren't
exactly similar (via a "warning") -- the function call itself should
be working and return a result to you, no?

This thread actually drew attention to the problem. Originally we were
getting an error in these situation, but Herve has now switched this
to a warning:
http://thread.gmane.org/gmane.science.biology.informatics.conductor/30491

Perhaps reading through that might shed more light on your issue, if
this is what you were asking about(?) If not, could you be a bit more
specific about the error/problem you are referring to?

Hope that helped,
-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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